13-27782185-T-C

Variant names:

• chr13-27782185-T-C
• rs1326384

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 0.432 in 152,110 control chromosomes in the GnomAD database, including 16,314 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 0.43 (16314 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65703 AN: 151994 Hom.: 16308 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.432 AC: 65734 AN: 152110 Hom.: 16314 Cov.: 32 AF XY: 0.443 AC XY: 32929 AN XY: 74348

African (AFR) AF: 0.182 AC: 7533 AN: 41500

American (AMR) AF: 0.468 AC: 7161 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1714 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3274 AN: 5174

South Asian (SAS) AF: 0.673 AC: 3242 AN: 4818

European-Finnish (FIN) AF: 0.563 AC: 5957 AN: 10576

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35181 AN: 67972

Other (OTH) AF: 0.463 AC: 976 AN: 2108

Alfa AF: 0.483 Hom.: 60009

Bravo AF: 0.409

Asia WGS AF: 0.630 AC: 2191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs1326384; hg19: chr13-28356322; COSMIC: COSV69345327;