13-27463278-C-T

Variant names:

• chr13-27463278-C-T
• rs1475219

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 0.794 in 152,176 control chromosomes in the GnomAD database, including 48,146 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 0.79 (48146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.872 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: 0.794 AC: 120785 AN: 152058 Hom.: 48110 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.794 AC: 120875 AN: 152176 Hom.: 48146 Cov.: 32 AF XY: 0.795 AC XY: 59101 AN XY: 74376

African (AFR) AF: 0.775 AC: 32171 AN: 41512

American (AMR) AF: 0.848 AC: 12964 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2940 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4219 AN: 5172

South Asian (SAS) AF: 0.894 AC: 4316 AN: 4828

European-Finnish (FIN) AF: 0.749 AC: 7921 AN: 10570

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53719 AN: 68012

Other (OTH) AF: 0.795 AC: 1678 AN: 2112

Alfa AF: 0.761 Hom.: 4025

Bravo AF: 0.801

Asia WGS AF: 0.840 AC: 2923 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	0.14
DANN	Benign	0.34
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1475219; hg19: chr13-28037415;