chr10-92382850-C-A

Variant names:

• chr10-92382850-C-A
• rs11186960

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 0.36 in 152,034 control chromosomes in the GnomAD database, including 12,514 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 0.36 (12514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 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: 0.361 AC: 54803 AN: 151916 Hom.: 12522 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.360 AC: 54788 AN: 152034 Hom.: 12514 Cov.: 32 AF XY: 0.352 AC XY: 26135 AN XY: 74304

African (AFR) AF: 0.116 AC: 4826 AN: 41502

American (AMR) AF: 0.367 AC: 5598 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3472

East Asian (EAS) AF: 0.102 AC: 531 AN: 5182

South Asian (SAS) AF: 0.232 AC: 1117 AN: 4806

European-Finnish (FIN) AF: 0.409 AC: 4320 AN: 10560

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35076 AN: 67932

Other (OTH) AF: 0.433 AC: 914 AN: 2112

Alfa AF: 0.391 Hom.: 9545

Bravo AF: 0.351

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.29
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs11186960; hg19: chr10-94142607;