13-69329601-G-C

Variant names:

• chr13-69329601-G-C
• rs2782448

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 0.703 in 151,866 control chromosomes in the GnomAD database, including 38,012 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 0.70 (38012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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: 0.703 AC: 106659 AN: 151748 Hom.: 37973 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.703 AC: 106758 AN: 151866 Hom.: 38012 Cov.: 32 AF XY: 0.695 AC XY: 51561 AN XY: 74194

African (AFR) AF: 0.801 AC: 33198 AN: 41426

American (AMR) AF: 0.729 AC: 11112 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2720 AN: 5152

South Asian (SAS) AF: 0.547 AC: 2634 AN: 4816

European-Finnish (FIN) AF: 0.640 AC: 6756 AN: 10550

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45874 AN: 67894

Other (OTH) AF: 0.676 AC: 1424 AN: 2108

Alfa AF: 0.583 Hom.: 1575

Bravo AF: 0.717

Asia WGS AF: 0.575 AC: 1998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.071
DANN	Benign	0.34
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2782448; hg19: chr13-69903733;