chr11-123747769-C-T

Variant names:

• chr11-123747769-C-T
• rs10893085

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 0.528 in 151,918 control chromosomes in the GnomAD database, including 21,710 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 0.53 (21710 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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: 0.528 AC: 80176 AN: 151800 Hom.: 21712 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.528 AC: 80195 AN: 151918 Hom.: 21710 Cov.: 31 AF XY: 0.520 AC XY: 38642 AN XY: 74248

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.547

Alfa AF: 0.546 Hom.: 8735

Bravo AF: 0.522

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10893085; hg19: chr11-123618477;