rs6432894

Variant names:

• chr2-166282470-A-C
• rs6432894
• NM_001365536.1:c.1975-662T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-166282470-A-C
• chr2-166282470-A-G
• chr2-166282470-A-T

Variant summary

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

The NM_001365536.1(SCN9A):​c.1975-662T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,040 control chromosomes in the GnomAD database, including 44,455 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 0.76 (44455 hom., cov: 31)
• Consequence: SCN9A NM_001365536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN9A	NM_001365536.1	c.1975-662T>G		intron_variant	Intron 12 of 26	ENST00000642356.2	NP_001352465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN9A	ENST00000642356.2	c.1975-662T>G		intron_variant	Intron 12 of 26		NM_001365536.1	ENSP00000495601.1
SCN9A	ENST00000303354.11	c.1975-662T>G		intron_variant	Intron 12 of 26	5		ENSP00000304748.7
SCN9A	ENST00000409672.5	c.1942-662T>G		intron_variant	Intron 12 of 26	5		ENSP00000386306.1
SCN9A	ENST00000645907.1	c.1942-662T>G		intron_variant	Intron 12 of 26			ENSP00000495983.1
SCN9A	ENST00000454569.6	c.1942-662T>G		intron_variant	Intron 12 of 14	1		ENSP00000413212.2

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114745 AN: 151922 Hom.: 44396 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.755 AC: 114864 AN: 152040 Hom.: 44455 Cov.: 31 AF XY: 0.755 AC XY: 56145 AN XY: 74322

African (AFR) AF: 0.932 AC: 38692 AN: 41522

American (AMR) AF: 0.689 AC: 10516 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2512 AN: 3466

East Asian (EAS) AF: 0.852 AC: 4406 AN: 5170

South Asian (SAS) AF: 0.772 AC: 3719 AN: 4820

European-Finnish (FIN) AF: 0.696 AC: 7358 AN: 10574

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45401 AN: 67908

Other (OTH) AF: 0.754 AC: 1592 AN: 2112

Alfa AF: 0.687 Hom.: 4198

Bravo AF: 0.761

Asia WGS AF: 0.823 AC: 2862 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		-0.62
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: rs6432894; hg19: chr2-167138980;