13-99594048-G-T

Variant names:

• chr13-99594048-G-T
• rs2763929

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 0.477 in 151,856 control chromosomes in the GnomAD database, including 17,519 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 (17519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 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: 0.477 AC: 72358 AN: 151738 Hom.: 17507 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.477 AC: 72404 AN: 151856 Hom.: 17519 Cov.: 32 AF XY: 0.475 AC XY: 35241 AN XY: 74214

African (AFR) AF: 0.394 AC: 16310 AN: 41356

American (AMR) AF: 0.509 AC: 7754 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1622 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1673 AN: 5172

South Asian (SAS) AF: 0.404 AC: 1945 AN: 4816

European-Finnish (FIN) AF: 0.523 AC: 5505 AN: 10524

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35820 AN: 67962

Other (OTH) AF: 0.523 AC: 1102 AN: 2108

Alfa AF: 0.374 Hom.: 1095

Bravo AF: 0.472

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.49
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2763929; hg19: chr13-100246302;