rs10893085

Variant names:

• chr11-123747769-C-T
• rs10893085

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.535 AC: 22157 AN: 41432

American (AMR) AF: 0.454 AC: 6932 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2060 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1050 AN: 5158

South Asian (SAS) AF: 0.423 AC: 2034 AN: 4808

European-Finnish (FIN) AF: 0.532 AC: 5609 AN: 10536

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38576 AN: 67948

Other (OTH) AF: 0.547 AC: 1153 AN: 2108

Alfa AF: 0.546 Hom.: 8859

Bravo AF: 0.522

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10893085; hg19: chr11-123618477;