1-156141496-A-G

Variant names:

• chr1-156141496-A-G
• rs536857

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 0.779 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.902 AC: 37424 AN: 41502

American (AMR) AF: 0.702 AC: 10744 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2454 AN: 3466

East Asian (EAS) AF: 0.752 AC: 3863 AN: 5136

South Asian (SAS) AF: 0.697 AC: 3360 AN: 4822

European-Finnish (FIN) AF: 0.805 AC: 8524 AN: 10592

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49709 AN: 67978

Other (OTH) AF: 0.763 AC: 1608 AN: 2108

Alfa AF: 0.749 Hom.: 35392

Bravo AF: 0.777

Asia WGS AF: 0.728 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs536857; hg19: chr1-156111287;