chr13-27776812-G-A

Variant names:

• chr13-27776812-G-A
• rs1326382

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 0.406 in 152,030 control chromosomes in the GnomAD database, including 12,692 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 0.41 (12692 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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: 0.406 AC: 61705 AN: 151912 Hom.: 12666 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.406 AC: 61781 AN: 152030 Hom.: 12692 Cov.: 33 AF XY: 0.407 AC XY: 30209 AN XY: 74296

African (AFR) AF: 0.368 AC: 15261 AN: 41470

American (AMR) AF: 0.383 AC: 5857 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1207 AN: 3464

East Asian (EAS) AF: 0.278 AC: 1436 AN: 5166

South Asian (SAS) AF: 0.402 AC: 1937 AN: 4814

European-Finnish (FIN) AF: 0.475 AC: 5012 AN: 10556

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29584 AN: 67960

Other (OTH) AF: 0.394 AC: 832 AN: 2114

Alfa AF: 0.427 Hom.: 8334

Bravo AF: 0.398

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.48
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs1326382; hg19: chr13-28350949;