Variant 3-38697226-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006514.4(SCN10A):c.*123C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 1,470,942 control chromosomes in the GnomAD database, including 147,134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 14628 hom., cov: 32)

Exomes 𝑓: 0.44 ( 132506 hom. )

Consequence

SCN10A
NM_006514.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.649

Variant links:

Genes affected

SCN10A (HGNC:10582): (sodium voltage-gated channel alpha subunit 10) The protein encoded by this gene is a tetrodotoxin-resistant voltage-gated sodium channel alpha subunit. The properties of the channel formed by the encoded transmembrane protein can be altered by interaction with different beta subunits. This protein may be involved in the onset of pain associated with peripheral neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

SCN10A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 3-38697226-G-A is Benign according to our data. Variant chr3-38697226-G-A is described in ClinVar as [Benign]. Clinvar id is 1259657.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
SCN10A	NM_006514.4 linkuse as main transcript	c.*123C>T	3_prime_UTR_variant	28/28	ENST00000449082.3	NP_006505.4
SCN10A	XM_005265371.4 linkuse as main transcript	c.*123C>T	3_prime_UTR_variant	27/27		XP_005265428.1
SCN10A	XM_011533993.3 linkuse as main transcript	c.*123C>T	3_prime_UTR_variant	27/27		XP_011532295.1
SCN10A	XM_011533994.3 linkuse as main transcript	c.*123C>T	3_prime_UTR_variant	26/26		XP_011532296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN10A	ENST00000449082.3 linkuse as main transcript	c.*123C>T		3_prime_UTR_variant	28/28	1	NM_006514.4	ENSP00000390600	P4
SCN10A	ENST00000655275.1 linkuse as main transcript	c.*123C>T		3_prime_UTR_variant	28/28			ENSP00000499510

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66303

AN:

151894

Hom.:

14636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.419

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.455

GnomAD4 exome

AF:

0.444

AC:

585843

AN:

1318930

Hom.:

132506

Cov.:

AF XY:

0.445

AC XY:

287556

AN XY:

646802

show subpopulations

Gnomad4 AFR exome

AF:

0.458

Gnomad4 AMR exome

AF:

0.375

Gnomad4 ASJ exome

AF:

0.417

Gnomad4 EAS exome

AF:

0.128

Gnomad4 SAS exome

AF:

0.434

Gnomad4 FIN exome

AF:

0.465

Gnomad4 NFE exome

AF:

0.458

Gnomad4 OTH exome

AF:

0.433

GnomAD4 genome

AF:

0.436

AC:

66308

AN:

152012

Hom.:

14628

Cov.:

AF XY:

0.432

AC XY:

32106

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.448

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.419

Gnomad4 EAS

AF:

0.138

Gnomad4 SAS

AF:

0.411

Gnomad4 FIN

AF:

0.477

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.452

Alfa

AF:

0.451

Hom.:

22803

Bravo

AF:

0.430

Asia WGS

AF:

0.297

AC:

1036

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

DANN

Benign

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over