rs10493953

Variant names:

• chr1-101457753-T-C
• rs10493953

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 0.0729 in 152,274 control chromosomes in the GnomAD database, including 574 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 0.073 (574 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 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: 0.0729 AC: 11085 AN: 152156 Hom.: 566 Cov.: 33

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.0727

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0692

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

GnomAD4 genome AF: 0.0729 AC: 11106 AN: 152274 Hom.: 574 Cov.: 33 AF XY: 0.0730 AC XY: 5432 AN XY: 74452

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0738

Gnomad4 OTH AF: 0.0685

Alfa AF: 0.0813 Hom.: 80

Bravo AF: 0.0798

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.3
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493953; hg19: chr1-101923309;