rs10743082

Variant names:

• chr11-8603448-C-T
• rs10743082

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 0.602 in 151,784 control chromosomes in the GnomAD database, including 27,841 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 0.60 (27841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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: 0.603 AC: 91384 AN: 151666 Hom.: 27827 Cov.: 31

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.602 AC: 91445 AN: 151784 Hom.: 27841 Cov.: 31 AF XY: 0.598 AC XY: 44395 AN XY: 74180

African (AFR) AF: 0.659 AC: 27275 AN: 41358

American (AMR) AF: 0.578 AC: 8813 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1657 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2396 AN: 5160

South Asian (SAS) AF: 0.423 AC: 2037 AN: 4812

European-Finnish (FIN) AF: 0.651 AC: 6854 AN: 10528

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.595 AC: 40374 AN: 67900

Other (OTH) AF: 0.560 AC: 1179 AN: 2104

Alfa AF: 0.602 Hom.: 12456

Bravo AF: 0.607

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.25
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10743082; hg19: chr11-8624995;