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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.582

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957828; hg19: chr1-84541716;