chr10-132386083-G-T

Variant names:

• chr10-132386083-G-T
• rs11146353

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 0.517 in 152,190 control chromosomes in the GnomAD database, including 21,875 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 0.52 (21875 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78658 AN: 152072 Hom.: 21839 Cov.: 34

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.517 AC: 78758 AN: 152190 Hom.: 21875 Cov.: 34 AF XY: 0.506 AC XY: 37679 AN XY: 74400

African (AFR) AF: 0.711 AC: 29494 AN: 41502

American (AMR) AF: 0.496 AC: 7590 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3470

East Asian (EAS) AF: 0.125 AC: 647 AN: 5184

South Asian (SAS) AF: 0.325 AC: 1568 AN: 4830

European-Finnish (FIN) AF: 0.363 AC: 3848 AN: 10606

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31960 AN: 67980

Other (OTH) AF: 0.526 AC: 1113 AN: 2116

Alfa AF: 0.460 Hom.: 5903

Bravo AF: 0.538

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11146353; hg19: chr10-134199587;