11-69639167-C-T

Variant names:

• chr11-69639167-C-T
• rs1944129

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 0.476 in 152,110 control chromosomes in the GnomAD database, including 17,711 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 (17711 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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: 0.476 AC: 72328 AN: 151990 Hom.: 17699 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.476 AC: 72372 AN: 152110 Hom.: 17711 Cov.: 33 AF XY: 0.479 AC XY: 35630 AN XY: 74368

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.499

Alfa AF: 0.340 Hom.: 1007

Bravo AF: 0.473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944129; hg19: chr11-69453935;