2-166241112-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365536.1(SCN9A):c.3627+1390T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,076 control chromosomes in the GnomAD database, including 52,289 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 0.83 (52289 hom., cov: 32)
• Consequence: SCN9A NM_001365536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN9A	NM_001365536.1	c.3627+1390T>C		intron_variant		ENST00000642356.2
SCN1A-AS1	NR_110260.1	n.612-7083A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN9A	ENST00000642356.2	c.3627+1390T>C		intron_variant			NM_001365536.1	P1
SCN1A-AS1	ENST00000651574.1	n.1290-7083A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125644 AN: 151958 Hom.: 52268 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.827 AC: 125717 AN: 152076 Hom.: 52289 Cov.: 32 AF XY: 0.827 AC XY: 61446 AN XY: 74342

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.824

Alfa AF: 0.848 Hom.: 6821

Bravo AF: 0.826

Asia WGS AF: 0.840 AC: 2920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.67

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

Other links and lift over

dbSNP: rs2155878; hg19: chr2-167097622;