rs10508743

Variant names:

• chr10-29135369-T-C
• rs10508743

Your query was ambiguous. Multiple possible variants found:

• chr10-29135369-T-C
• chr10-29135369-T-G

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 0.25 in 152,100 control chromosomes in the GnomAD database, including 5,078 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 0.25 (5078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.250 AC: 37969 AN: 151984 Hom.: 5064 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.250 AC: 38001 AN: 152100 Hom.: 5078 Cov.: 32 AF XY: 0.249 AC XY: 18526 AN XY: 74348

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.217

Alfa AF: 0.266 Hom.: 9540

Bravo AF: 0.252

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508743; hg19: chr10-29424298;