rs536857

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;