rs10497281

chr2-166159592-A-Gchr2-166159592-A-T

Variant summary

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

The NR_110260.1(SCN1A-AS1):n.260-11795A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 152,248 control chromosomes in the GnomAD database, including 646 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 0.041 (646 hom., cov: 32)
• Consequence: SCN1A-AS1 NR_110260.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

Genes affected

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN1A-AS1	NR_110260.1	n.260-11795A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN1A-AS1	ENST00000651574.1	n.938-11795A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6190 AN: 152128 Hom.: 643 Cov.: 32

Gnomad AFR AF: 0.00750

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0407 AC: 6200 AN: 152248 Hom.: 646 Cov.: 32 AF XY: 0.0457 AC XY: 3403 AN XY: 74436

Gnomad4 AFR AF: 0.00748

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.0174

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0298 Hom.: 545

Bravo AF: 0.0560

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.9
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497281; hg19: chr2-167016102;