10-2135668-C-T

Position:

• chr10-2135668-C-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 0.657 in 152,030 control chromosomes in the GnomAD database, including 35,215 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 0.66 (35215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.657 AC: 99817 AN: 151910 Hom.: 35213 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.657 AC: 99859 AN: 152030 Hom.: 35215 Cov.: 32 AF XY: 0.660 AC XY: 49047 AN XY: 74288

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.687

Alfa AF: 0.688 Hom.: 6372

Bravo AF: 0.631

Asia WGS AF: 0.780 AC: 2709 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	2.4
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2210553; hg19: chr10-2177862;