2-166303300-GG-AT

Position:

• chr2-166303300-GG-AT

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP6_Moderate BP7

The NM_001365536.1(SCN9A):​c.690_691delCCinsAT​(p.232) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SCN9A NM_001365536.1 splice_region, synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.20

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 Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 2-166303300-GG-AT is Benign according to our data. Variant chr2-166303300-GG-AT is described in ClinVar as [Likely_benign]. Clinvar id is 471162.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=1.2 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN9A	NM_001365536.1	c.690_691delCCinsAT	p.232	splice_region_variant, synonymous_variant		ENST00000642356.2	NP_001352465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN9A	ENST00000642356.2	c.690_691delCCinsAT	p.232	splice_region_variant, synonymous_variant			NM_001365536.1	ENSP00000495601.1
SCN9A	ENST00000303354.11	c.690_691delCCinsAT	p.232	splice_region_variant, synonymous_variant		5		ENSP00000304748.7
SCN9A	ENST00000409672.5	c.690_691delCCinsAT	p.232	splice_region_variant, synonymous_variant		5		ENSP00000386306.1
SCN9A	ENST00000645907.1	c.690_691delCCinsAT	p.232	splice_region_variant, synonymous_variant				ENSP00000495983.1
SCN9A	ENST00000454569.6	c.690_691delCCinsAT	p.232	splice_region_variant, synonymous_variant		1		ENSP00000413212.2
SCN9A	ENST00000452182.2	c.690_691delCCinsAT	p.232	splice_region_variant, synonymous_variant		1		ENSP00000393141.2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Generalized epilepsy with febrile seizures plus, type 7;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 03, 2017

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1553495271; hg19: chr2-167159810;