rs1169791

Variant names:

• chr13-42696381-C-T
• rs1169791

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 0.485 in 151,980 control chromosomes in the GnomAD database, including 19,181 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 0.48 (19181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 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: 0.485 AC: 73664 AN: 151862 Hom.: 19171 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.485 AC: 73690 AN: 151980 Hom.: 19181 Cov.: 32 AF XY: 0.483 AC XY: 35847 AN XY: 74290

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.505

Alfa AF: 0.577 Hom.: 51933

Bravo AF: 0.467

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1169791; hg19: chr13-43270517;