rs536857

Variant names:

• chr1-156141496-A-G
• rs536857

Your query was ambiguous. Multiple possible variants found:

• chr1-156141496-A-G
• chr1-156141496-A-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 0.779 in 152,108 control chromosomes in the GnomAD database, including 46,762 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 0.78 (46762 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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: 0.779 AC: 118411 AN: 151988 Hom.: 46719 Cov.: 31

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.779 AC: 118511 AN: 152108 Hom.: 46762 Cov.: 31 AF XY: 0.779 AC XY: 57929 AN XY: 74352

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.763

Alfa AF: 0.740 Hom.: 25637

Bravo AF: 0.777

Asia WGS AF: 0.728 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs536857; hg19: chr1-156111287;