rs1326382

Variant names:

• chr13-27776812-G-A
• rs1326382

Your query was ambiguous. Multiple possible variants found:

• chr13-27776812-G-A
• chr13-27776812-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 0.406 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.394

Alfa AF: 0.427 Hom.: 7563

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1326382; hg19: chr13-28350949;