rs744536

Variant names:

• chr1-151356318-T-A
• rs744536

Your query was ambiguous. Multiple possible variants found:

• chr1-151356318-T-A
• chr1-151356318-T-C
• chr1-151356318-T-G

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 0.578 in 152,020 control chromosomes in the GnomAD database, including 25,926 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 0.58 (25926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.579 AC: 87900 AN: 151902 Hom.: 25929 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.578 AC: 87927 AN: 152020 Hom.: 25926 Cov.: 32 AF XY: 0.572 AC XY: 42488 AN XY: 74290

African (AFR) AF: 0.473 AC: 19588 AN: 41452

American (AMR) AF: 0.579 AC: 8833 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2012 AN: 3472

East Asian (EAS) AF: 0.585 AC: 3021 AN: 5160

South Asian (SAS) AF: 0.627 AC: 3023 AN: 4820

European-Finnish (FIN) AF: 0.535 AC: 5643 AN: 10548

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43673 AN: 67988

Other (OTH) AF: 0.602 AC: 1269 AN: 2108

Alfa AF: 0.598 Hom.: 3229

Bravo AF: 0.578

Asia WGS AF: 0.649 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.72
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs744536; hg19: chr1-151328794;