rs2256956

Variant names:

• chr1-182350800-G-A
• rs2256956

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 0.67 in 152,076 control chromosomes in the GnomAD database, including 34,697 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 0.67 (34697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101856 AN: 151958 Hom.: 34646 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.670 AC: 101951 AN: 152076 Hom.: 34697 Cov.: 32 AF XY: 0.665 AC XY: 49469 AN XY: 74342

African (AFR) AF: 0.777 AC: 32243 AN: 41474

American (AMR) AF: 0.606 AC: 9248 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2465 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2396 AN: 5170

South Asian (SAS) AF: 0.685 AC: 3305 AN: 4828

European-Finnish (FIN) AF: 0.589 AC: 6228 AN: 10572

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43871 AN: 67978

Other (OTH) AF: 0.668 AC: 1413 AN: 2116

Alfa AF: 0.654 Hom.: 139664

Bravo AF: 0.673

Asia WGS AF: 0.639 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.43
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2256956; hg19: chr1-182319935;