rs10893085

chr11-123747769-C-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 0.528 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;