10-2135668-C-T

Variant names:

• chr10-2135668-C-T
• rs2210553

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;