13-27789305-G-T

Variant names:

• chr13-27789305-G-T
• rs1231054

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 0.472 in 152,052 control chromosomes in the GnomAD database, including 17,125 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 0.47 (17125 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 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: 0.472 AC: 71688 AN: 151934 Hom.: 17107 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.472 AC: 71767 AN: 152052 Hom.: 17125 Cov.: 33 AF XY: 0.479 AC XY: 35564 AN XY: 74318

African (AFR) AF: 0.426 AC: 17685 AN: 41470

American (AMR) AF: 0.542 AC: 8277 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2407 AN: 5150

South Asian (SAS) AF: 0.652 AC: 3149 AN: 4832

European-Finnish (FIN) AF: 0.492 AC: 5199 AN: 10566

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32016 AN: 67964

Other (OTH) AF: 0.489 AC: 1034 AN: 2116

Alfa AF: 0.467 Hom.: 18036

Bravo AF: 0.469

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.70
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs1231054; hg19: chr13-28363442;