rs80356466

Variant names:

• chr2-166304310-T-C
• rs80356466
• NM_001365536.1:c.616A>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001365536.1(SCN9A):​c.616A>G​(p.Asn206Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SCN9A NM_001365536.1 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 6.15

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCN9A	NM_001365536.1	c.616A>G	p.Asn206Asp	missense_variant	Exon 6 of 27	ENST00000642356.2	NP_001352465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCN9A	ENST00000642356.2	c.616A>G	p.Asn206Asp	missense_variant	Exon 6 of 27		NM_001365536.1	ENSP00000495601.1
SCN9A	ENST00000303354.11	c.616A>G	p.Asn206Asp	missense_variant	Exon 6 of 27	5		ENSP00000304748.7
SCN9A	ENST00000409672.5	c.616A>G	p.Asn206Asp	missense_variant	Exon 6 of 27	5		ENSP00000386306.1
SCN9A	ENST00000454569.6	c.616A>G	p.Asn206Asp	missense_variant	Exon 6 of 15	1		ENSP00000413212.2
SCN9A	ENST00000452182.2	c.616A>G	p.Asn206Asp	missense_variant	Exon 7 of 11	1		ENSP00000393141.2
SCN9A	ENST00000645907.1	c.597-188A>G		intron_variant	Intron 5 of 26			ENSP00000495983.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

Primary erythromelalgia Other:1

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.053
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.070
CADD	Benign	21
DANN	Benign	0.88
DEOGEN2	Benign	0.41	.;T;T;.;.
Eigen	Benign	-0.34
Eigen_PC	Benign	-0.032
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.76	T;.;T;T;T
M_CAP	Benign	0.029	D
MetaRNN	Uncertain	0.45	T;T;T;T;T
MetaSVM	Uncertain	0.28	D
MutationAssessor	Benign	-0.56	N;N;N;.;.
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	2.1	N;.;.;.;.
REVEL	Uncertain	0.39
Sift	Benign	1.0	T;.;.;.;.
Sift4G	Benign	1.0	T;T;.;.;.
Vest4		0.63
MutPred		0.73		Loss of helix (P = 0.0626);Loss of helix (P = 0.0626);Loss of helix (P = 0.0626);Loss of helix (P = 0.0626);Loss of helix (P = 0.0626);
MVP		0.74
MPC		0.13
ClinPred		0.92	D
GERP RS		5.8
Varity_R		0.25
gMVP		0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs80356466; hg19: chr2-167160820;