rs4644762

Variant names:

• chr13-86039253-T-A
• rs4644762

Your query was ambiguous. Multiple possible variants found:

• chr13-86039253-T-A
• chr13-86039253-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 0.524 in 151,598 control chromosomes in the GnomAD database, including 21,572 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 0.52 (21572 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 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: 0.524 AC: 79388 AN: 151480 Hom.: 21554 Cov.: 30

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.524 AC: 79453 AN: 151598 Hom.: 21572 Cov.: 30 AF XY: 0.528 AC XY: 39051 AN XY: 74022

African (AFR) AF: 0.386 AC: 15974 AN: 41330

American (AMR) AF: 0.466 AC: 7096 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1601 AN: 3472

East Asian (EAS) AF: 0.602 AC: 3070 AN: 5100

South Asian (SAS) AF: 0.512 AC: 2452 AN: 4788

European-Finnish (FIN) AF: 0.708 AC: 7425 AN: 10482

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.590 AC: 40078 AN: 67896

Other (OTH) AF: 0.503 AC: 1057 AN: 2100

Alfa AF: 0.469 Hom.: 1496

Bravo AF: 0.500

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.13
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4644762; hg19: chr13-86613388;