rs957828

chr1-84076033-C-Achr1-84076033-C-Gchr1-84076033-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;