Variant rs13017637 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001365536.1(SCN9A):c.689-134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 660,158 control chromosomes in the GnomAD database, including 57,326 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 11169 hom., cov: 32)

Exomes 𝑓: 0.42 ( 46157 hom. )

Consequence

SCN9A
NM_001365536.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650

Variant links:

Genes affected

SCN9A (HGNC:10597): (sodium voltage-gated channel alpha subunit 9) This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]

SCN9A links:

SCN1A-AS1 (HGNC:54069): (SCN1A and SCN9A antisense RNA 1)

SCN1A-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN9A	NM_001365536.1 linkuse as main transcript	c.689-134G>A		intron_variant		ENST00000642356.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN9A	ENST00000642356.2 linkuse as main transcript	c.689-134G>A		intron_variant			NM_001365536.1	P1	Q15858-1
SCN1A-AS1	ENST00000651574.1 linkuse as main transcript	n.1977+7307C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55871

AN:

151844

Hom.:

11173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.443

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.364

GnomAD4 exome

AF:

0.416

AC:

211447

AN:

508196

Hom.:

46157

AF XY:

0.417

AC XY:

112432

AN XY:

269894

show subpopulations

Gnomad4 AFR exome

AF:

0.239

Gnomad4 AMR exome

AF:

0.314

Gnomad4 ASJ exome

AF:

0.451

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.395

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.449

Gnomad4 OTH exome

AF:

0.413

GnomAD4 genome

AF:

0.368

AC:

55879

AN:

151962

Hom.:

11169

Cov.:

AF XY:

0.366

AC XY:

27142

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.339

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.177

Gnomad4 SAS

AF:

0.389

Gnomad4 FIN

AF:

0.451

Gnomad4 NFE

AF:

0.453

Gnomad4 OTH

AF:

0.363

Alfa

AF:

0.421

Hom.:

12892

Bravo

AF:

0.347

Asia WGS

AF:

0.299

AC:

1042

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.6

DANN

Benign

0.57

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over