Variant chr2-166196045-CTTAAAAAAGTT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001365536.1(SCN9A):c.*2616_*2626del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,348 control chromosomes in the GnomAD database, including 17,861 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.48 ( 17859 hom., cov: 0)

Exomes 𝑓: 0.50 ( 2 hom. )

Consequence

SCN9A
NM_001365536.1 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:7

Conservation

PhyloP100: 1.70

Variant links:

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]

SCN9A links:

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

SCN1A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 2-166196045-CTTAAAAAAGTT-C is Benign according to our data. Variant chr2-166196045-CTTAAAAAAGTT-C is described in ClinVar as [Benign]. Clinvar id is 331908.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN9A	NM_001365536.1 linkuse as main transcript	c.2616_2626del		3_prime_UTR_variant	27/27	ENST00000642356.2	NP_001352465.1
SCN1A-AS1	NR_110260.1 linkuse as main transcript	n.432-3591_432-3581del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN9A	ENST00000642356.2 linkuse as main transcript	c.2616_2626del		3_prime_UTR_variant	27/27		NM_001365536.1	ENSP00000495601	P1	Q15858-1
SCN1A-AS1	ENST00000651574.1 linkuse as main transcript	n.1110-3591_1110-3581del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

72888

AN:

151206

Hom.:

17854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.475

Gnomad OTH

AF:

0.469

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.482

AC:

72916

AN:

151326

Hom.:

17859

Cov.:

AF XY:

0.476

AC XY:

35225

AN XY:

73928

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.353

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.431

Gnomad4 SAS

AF:

0.469

Gnomad4 FIN

AF:

0.454

Gnomad4 NFE

AF:

0.475

Gnomad4 OTH

AF:

0.467

Alfa

AF:

0.492

Hom.:

2236

Bravo

AF:

0.481

Asia WGS

AF:

0.460

AC:

1601

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Inherited Erythromelalgia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Generalized epilepsy with febrile seizures plus

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Congenital Indifference to Pain

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Small fiber neuropathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Paroxysmal extreme pain disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Febrile seizures, familial

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Severe myoclonic epilepsy in infancy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over