chr13-80094739-T-C

Variant names:

• chr13-80094739-T-C
• rs9574565

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.653 in 151,994 control chromosomes in the GnomAD database, including 34,133 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 0.65 (34133 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.653 AC: 99150 AN: 151876 Hom.: 34131 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.653 AC: 99188 AN: 151994 Hom.: 34133 Cov.: 31 AF XY: 0.650 AC XY: 48316 AN XY: 74286

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.693

Alfa AF: 0.734 Hom.: 64195

Bravo AF: 0.656

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9574565; hg19: chr13-80668874;