rs2343331

Variant names:

• chr1-162961030-C-T
• rs2343331

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.24 in 152,044 control chromosomes in the GnomAD database, including 4,658 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 0.24 (4658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36477 AN: 151926 Hom.: 4660 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.240 AC: 36481 AN: 152044 Hom.: 4658 Cov.: 32 AF XY: 0.236 AC XY: 17553 AN XY: 74324

African (AFR) AF: 0.172 AC: 7141 AN: 41456

American (AMR) AF: 0.232 AC: 3538 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 747 AN: 3466

East Asian (EAS) AF: 0.150 AC: 775 AN: 5170

South Asian (SAS) AF: 0.132 AC: 636 AN: 4822

European-Finnish (FIN) AF: 0.315 AC: 3321 AN: 10556

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19555 AN: 67986

Other (OTH) AF: 0.232 AC: 490 AN: 2110

Alfa AF: 0.265 Hom.: 2896

Bravo AF: 0.233

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs2343331; hg19: chr1-162930820;