rs957828

Variant names:

• chr1-84076033-C-A
• rs957828

Your query was ambiguous. Multiple possible variants found:

• chr1-84076033-C-A
• chr1-84076033-C-G
• chr1-84076033-C-T

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 0.566 in 151,898 control chromosomes in the GnomAD database, including 25,461 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 0.57 (25461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 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: 0.566 AC: 85844 AN: 151780 Hom.: 25433 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.566 AC: 85924 AN: 151898 Hom.: 25461 Cov.: 32 AF XY: 0.561 AC XY: 41639 AN XY: 74230

African (AFR) AF: 0.424 AC: 17571 AN: 41438

American (AMR) AF: 0.514 AC: 7847 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2046 AN: 5174

South Asian (SAS) AF: 0.534 AC: 2576 AN: 4820

European-Finnish (FIN) AF: 0.632 AC: 6657 AN: 10538

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.669 AC: 45388 AN: 67892

Other (OTH) AF: 0.582 AC: 1227 AN: 2108

Alfa AF: 0.611 Hom.: 4264

Bravo AF: 0.547

Asia WGS AF: 0.510 AC: 1754 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.39
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs957828; hg19: chr1-84541716;