rs1512651

chr13-56198562-G-Achr13-56198562-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;