rs587780895

Variant names:

• chr16-28477729-A-G
• rs587780895
• NM_001042432.2:c.1197+8T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 2P and 12B. PM2 BP4_Strong BP6_Very_Strong

The NM_001042432.2(CLN3):​c.1197+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: CLN3 NM_001042432.2 splice_region, intron
• Scores: Splicing: ADA: 0.00001556
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.727
• Publications: 0 publications found

Genes affected

CLN3 (HGNC:2074): (CLN3 lysosomal/endosomal transmembrane protein, battenin) This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

CLN3 Gene-Disease associations (from GenCC):

• inherited retinal dystrophy

  Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
• neuronal ceroid lipofuscinosis

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• neuronal ceroid lipofuscinosis 3

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae), Myriad Women’s Health

ENSG00000261832 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 16-28477729-A-G is Benign according to our data. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-28477729-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 136784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLN3	NM_001042432.2	c.1197+8T>C		splice_region_variant, intron_variant	Intron 15 of 15	ENST00000636147.2	NP_001035897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLN3	ENST00000636147.2	c.1197+8T>C		splice_region_variant, intron_variant	Intron 15 of 15	1	NM_001042432.2	ENSP00000490105.1
ENSG00000261832	ENST00000637378.1	c.228+4376T>C		intron_variant	Intron 4 of 9	5		ENSP00000490831.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000312 Hom.: 0

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Mar 13, 2014

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Neuronal ceroid lipofuscinosis Benign:1

Mar 10, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.49
PhyloP100		0.73

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000016
dbscSNV1_RF	Benign	0.0
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587780895; hg19: chr16-28489050;