13-91344502-T-C

Variant names:

• chr13-91344502-T-C
• rs17642969

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 0.0788 in 152,036 control chromosomes in the GnomAD database, including 574 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 0.079 (574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0968 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: 0.0786 AC: 11948 AN: 151918 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0660

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0788 AC: 11979 AN: 152036 Hom.: 574 Cov.: 32 AF XY: 0.0771 AC XY: 5731 AN XY: 74332

African (AFR) AF: 0.0563 AC: 2340 AN: 41534

American (AMR) AF: 0.0582 AC: 889 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.0661 AC: 319 AN: 4828

European-Finnish (FIN) AF: 0.0786 AC: 833 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0988 AC: 6697 AN: 67812

Other (OTH) AF: 0.0842 AC: 178 AN: 2114

Alfa AF: 0.0945 Hom.: 197

Bravo AF: 0.0744

Asia WGS AF: 0.0370 AC: 129 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.50
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17642969; hg19: chr13-91996756;