11-63630800-C-CAA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_015459.5(ATL3):c.1539+239_1539+240insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.012 (14 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: ATL3 NM_015459.5 intron
• Clinical Significance: Likely 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 11-63630800-C-CAA is Benign according to our data. Variant chr11-63630800-C-CAA is described in ClinVar as [Likely_benign]. Clinvar id is 1300681.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 1307 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATL3	NM_015459.5	c.1539+239_1539+240insTT		intron_variant		ENST00000398868.8
ATL3	NM_001290048.2	c.1485+239_1485+240insTT		intron_variant
ATL3	XM_006718493.2	c.1482+239_1482+240insTT		intron_variant
ATL3	XM_047426725.1	c.1695+239_1695+240insTT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATL3	ENST00000398868.8	c.1539+239_1539+240insTT		intron_variant		1	NM_015459.5
ATL3	ENST00000538786.1	c.1485+239_1485+240insTT		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0119 AC: 1307 AN: 109894 Hom.: 14 Cov.: 0

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00604

Gnomad ASJ AF: 0.00294

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000302

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000175

Gnomad OTH AF: 0.00974

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0119 AC: 1310 AN: 109888 Hom.: 14 Cov.: 0 AF XY: 0.0122 AC XY: 634 AN XY: 52054

Gnomad4 AFR AF: 0.0407

Gnomad4 AMR AF: 0.00604

Gnomad4 ASJ AF: 0.00294

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000304

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000175

Gnomad4 OTH AF: 0.00971

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;