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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.485 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

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.518

Alfa AF: 0.546 Hom.: 51597

Bravo AF: 0.480

Asia WGS AF: 0.506 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1512651; hg19: chr13-56772696;