rs1512651

Variant names:

• chr13-56198562-G-A
• rs1512651

Your query was ambiguous. Multiple possible variants found:

• chr13-56198562-G-A
• chr13-56198562-G-T

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 0.484 in 151,618 control chromosomes in the GnomAD database, including 19,155 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 0.48 (19155 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.947
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73417 AN: 151500 Hom.: 19163 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.484 AC: 73422 AN: 151618 Hom.: 19155 Cov.: 31 AF XY: 0.488 AC XY: 36187 AN XY: 74084

African (AFR) AF: 0.283 AC: 11697 AN: 41392

American (AMR) AF: 0.567 AC: 8614 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1970 AN: 3456

East Asian (EAS) AF: 0.615 AC: 3134 AN: 5098

South Asian (SAS) AF: 0.431 AC: 2073 AN: 4808

European-Finnish (FIN) AF: 0.627 AC: 6625 AN: 10566

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37500 AN: 67812

Other (OTH) AF: 0.518 AC: 1087 AN: 2100

Alfa AF: 0.532 Hom.: 75523

Bravo AF: 0.480

Asia WGS AF: 0.506 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs1512651; hg19: chr13-56772696;