chr13-79594869-C-T

Variant names:

• chr13-79594869-C-T
• rs9601248

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 0.539 in 151,832 control chromosomes in the GnomAD database, including 22,639 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 0.54 (22639 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.538 AC: 81681 AN: 151714 Hom.: 22598 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.539 AC: 81787 AN: 151832 Hom.: 22639 Cov.: 31 AF XY: 0.536 AC XY: 39798 AN XY: 74214

African (AFR) AF: 0.645 AC: 26721 AN: 41404

American (AMR) AF: 0.617 AC: 9420 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2242 AN: 5164

South Asian (SAS) AF: 0.376 AC: 1810 AN: 4812

European-Finnish (FIN) AF: 0.464 AC: 4872 AN: 10508

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33156 AN: 67904

Other (OTH) AF: 0.545 AC: 1151 AN: 2110

Alfa AF: 0.504 Hom.: 73969

Bravo AF: 0.556

Asia WGS AF: 0.432 AC: 1505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.39
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs9601248; hg19: chr13-80169004;