13-27789305-G-T

Variant names:

• chr13-27789305-G-T
• rs1231054

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;