13-27025437-T-C

Variant names:

• chr13-27025437-T-C
• rs2479561

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 0.669 in 152,018 control chromosomes in the GnomAD database, including 34,730 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 0.67 (34730 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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: 0.669 AC: 101566 AN: 151900 Hom.: 34696 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.669 AC: 101663 AN: 152018 Hom.: 34730 Cov.: 31 AF XY: 0.673 AC XY: 49985 AN XY: 74284

African (AFR) AF: 0.762 AC: 31605 AN: 41468

American (AMR) AF: 0.702 AC: 10732 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1894 AN: 3468

East Asian (EAS) AF: 0.969 AC: 5022 AN: 5184

South Asian (SAS) AF: 0.668 AC: 3210 AN: 4808

European-Finnish (FIN) AF: 0.625 AC: 6590 AN: 10548

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40656 AN: 67958

Other (OTH) AF: 0.663 AC: 1393 AN: 2102

Alfa AF: 0.597 Hom.: 5517

Bravo AF: 0.683

Asia WGS AF: 0.807 AC: 2806 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	1.4
DANN	Benign	0.22
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs2479561; hg19: chr13-27599574;