2-166314680-C-T

Variant names:

• chr2-166314680-C-T
• rs6760472
• NM_001365536.1:c.-50-2874G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365536.1(SCN9A):​c.-50-2874G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,104 control chromosomes in the GnomAD database, including 36,804 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 0.68 (36804 hom., cov: 32)
• Consequence: SCN9A NM_001365536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 5 publications found

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN9A	NM_001365536.1	c.-50-2874G>A		intron_variant	Intron 1 of 26	ENST00000642356.2	NP_001352465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN9A	ENST00000642356.2	c.-50-2874G>A		intron_variant	Intron 1 of 26		NM_001365536.1	ENSP00000495601.1
SCN9A	ENST00000303354.11	c.-50-2874G>A		intron_variant	Intron 1 of 26	5		ENSP00000304748.7
SCN9A	ENST00000409672.5	c.-50-2874G>A		intron_variant	Intron 1 of 26	5		ENSP00000386306.1
SCN9A	ENST00000645907.1	c.-50-2874G>A		intron_variant	Intron 1 of 26			ENSP00000495983.1
SCN9A	ENST00000454569.6	c.-50-2874G>A		intron_variant	Intron 1 of 14	1		ENSP00000413212.2
SCN9A	ENST00000452182.2	c.-50-2874G>A		intron_variant	Intron 2 of 10	1		ENSP00000393141.2

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103686 AN: 151984 Hom.: 36745 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.682 AC: 103792 AN: 152104 Hom.: 36804 Cov.: 32 AF XY: 0.672 AC XY: 49984 AN XY: 74332

African (AFR) AF: 0.877 AC: 36455 AN: 41554

American (AMR) AF: 0.574 AC: 8767 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5158

South Asian (SAS) AF: 0.561 AC: 2704 AN: 4822

European-Finnish (FIN) AF: 0.558 AC: 5882 AN: 10540

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43809 AN: 67968

Other (OTH) AF: 0.672 AC: 1420 AN: 2114

Alfa AF: 0.655 Hom.: 12726

Bravo AF: 0.689

Asia WGS AF: 0.520 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.77
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6760472; hg19: chr2-167171190;