11-63630800-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015459.5(ATL3):c.1539+239del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.87 (41126 hom., cov: 0)
• Consequence: ATL3 NM_015459.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.39

Genes affected

ATL3 (HGNC:24526): (atlastin GTPase 3) This gene encodes a member of a family of dynamin-like, integral membrane GTPases. The encoded protein is required for the proper formation of the network of interconnected tubules of the endoplasmic reticulum. Mutations in this gene may be associated with hereditary sensory neuropathy type IF. Alternatively spliced transcript variants that encode distinct isoforms have been described. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-63630800-CA-C is Benign according to our data. Variant chr11-63630800-CA-C is described in ClinVar as [Benign]. Clinvar id is 1292580.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATL3	NM_015459.5	c.1539+239del		intron_variant		ENST00000398868.8
ATL3	NM_001290048.2	c.1485+239del		intron_variant
ATL3	XM_006718493.2	c.1482+239del		intron_variant
ATL3	XM_047426725.1	c.1695+239del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATL3	ENST00000398868.8	c.1539+239del		intron_variant		1	NM_015459.5
ATL3	ENST00000538786.1	c.1485+239del		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.870 AC: 95725 AN: 110002 Hom.: 41141 Cov.: 0

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.961

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.886

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.870 AC: 95705 AN: 109994 Hom.: 41126 Cov.: 0 AF XY: 0.873 AC XY: 45489 AN XY: 52108

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.887

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
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

Publications

LitVar

Other links and lift over

dbSNP: rs58752695; hg19: chr11-63398272;