1-101457753-T-C

Variant names:

• chr1-101457753-T-C
• rs10493953

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0439 AC: 1824 AN: 41558

American (AMR) AF: 0.173 AC: 2636 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3472

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5190

South Asian (SAS) AF: 0.109 AC: 524 AN: 4826

European-Finnish (FIN) AF: 0.0554 AC: 588 AN: 10618

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0738 AC: 5023 AN: 68018

Other (OTH) AF: 0.0685 AC: 145 AN: 2116

Alfa AF: 0.0805 Hom.: 82

Bravo AF: 0.0798

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.3
DANN	Benign	0.77
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10493953; hg19: chr1-101923309;