13-27789305-G-T

Position:

• chr13-27789305-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.489

Alfa AF: 0.467 Hom.: 13160

Bravo AF: 0.469

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1231054; hg19: chr13-28363442;