rs10493953

Positions:

• chr1-101457753-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;