10-132386083-G-T

Position:

• chr10-132386083-G-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 0.517 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.526

Alfa AF: 0.443 Hom.: 4304

Bravo AF: 0.538

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11146353; hg19: chr10-134199587;