rs72471101

Variant names:

• chr2-165176265-CATT-C
• rs72471101
• NM_006922.4:c.127_129delAAT

Your query was ambiguous. Multiple possible variants found:

• chr2-165176265-CATT-C
• chr2-165176265-CATT-CATTATT

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_Supporting BP6_Very_Strong BA1

The NM_006922.4(SCN3A):​c.127_129delAAT​(p.Asn43del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 1,613,962 control chromosomes in the GnomAD database, including 7,425 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.083 (641 hom., cov: 31)
  • Exomes 𝑓: 0.091 (6784 hom.)
• Consequence: SCN3A NM_006922.4 conservative_inframe_deletion
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: 1.78

Genes affected

SCN3A (HGNC:10590): (sodium voltage-gated channel alpha subunit 3) Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000236283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -15 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_006922.4. Strenght limited to Supporting due to length of the change: 1aa.
• BP6: Variant 2-165176265-CATT-C is Benign according to our data. Variant chr2-165176265-CATT-C is described in ClinVar as [Benign]. Clinvar id is 95444.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN3A	NM_006922.4	c.127_129delAAT	p.Asn43del	conservative_inframe_deletion	Exon 3 of 28	ENST00000283254.12	NP_008853.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN3A	ENST00000283254.12	c.127_129delAAT	p.Asn43del	conservative_inframe_deletion	Exon 3 of 28	1	NM_006922.4	ENSP00000283254.7

Frequencies

GnomAD3 genomes AF: 0.0831 AC: 12627 AN: 152024 Hom.: 641 Cov.: 31

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0402

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.0727

GnomAD3 exomes AF: 0.0840 AC: 21119 AN: 251438 Hom.: 1131 AF XY: 0.0873 AC XY: 11863 AN XY: 135892

Gnomad AFR exome AF: 0.0559

Gnomad AMR exome AF: 0.0323

Gnomad ASJ exome AF: 0.116

Gnomad EAS exome AF: 0.00120

Gnomad SAS exome AF: 0.0830

Gnomad FIN exome AF: 0.178

Gnomad NFE exome AF: 0.0965

Gnomad OTH exome AF: 0.0872

GnomAD4 exome AF: 0.0906 AC: 132502 AN: 1461820 Hom.: 6784 AF XY: 0.0911 AC XY: 66228 AN XY: 727214

Gnomad4 AFR exome AF: 0.0591

Gnomad4 AMR exome AF: 0.0323

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.000579

Gnomad4 SAS exome AF: 0.0856

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.0930

Gnomad4 OTH exome AF: 0.0888

GnomAD4 genome AF: 0.0831 AC: 12636 AN: 152142 Hom.: 641 Cov.: 31 AF XY: 0.0850 AC XY: 6324 AN XY: 74364

Gnomad4 AFR AF: 0.0591

Gnomad4 AMR AF: 0.0402

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0783

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.0964

Gnomad4 OTH AF: 0.0715

Alfa AF: 0.0994 Hom.: 157

Bravo AF: 0.0707

Asia WGS AF: 0.0350 AC: 122 AN: 3478

EpiCase AF: 0.0901

EpiControl AF: 0.0888

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 20, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 09, 2022

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

See Variant Classification Assertion Criteria. -

not specified Benign:1

May 09, 2013

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Epilepsy, familial focal, with variable foci 4 Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Developmental and epileptic encephalopathy, 62 Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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: rs72471101; hg19: chr2-166032775;