13-27811620-C-T

Variant names:

• chr13-27811620-C-T
• rs9512879

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 0.842 in 152,126 control chromosomes in the GnomAD database, including 54,496 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 0.84 (54496 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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: 0.842 AC: 128058 AN: 152008 Hom.: 54450 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.842 AC: 128158 AN: 152126 Hom.: 54496 Cov.: 31 AF XY: 0.836 AC XY: 62189 AN XY: 74380

African (AFR) AF: 0.949 AC: 39417 AN: 41520

American (AMR) AF: 0.824 AC: 12604 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3792 AN: 5162

South Asian (SAS) AF: 0.624 AC: 2999 AN: 4808

European-Finnish (FIN) AF: 0.785 AC: 8303 AN: 10576

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55616 AN: 67982

Other (OTH) AF: 0.818 AC: 1727 AN: 2112

Alfa AF: 0.829 Hom.: 42579

Bravo AF: 0.856

Asia WGS AF: 0.641 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.25
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs9512879; hg19: chr13-28385757;