10-127514427-T-C

Variant names:

• chr10-127514427-T-C
• rs1572237

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 0.813 in 152,144 control chromosomes in the GnomAD database, including 50,405 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 0.81 (50405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123614 AN: 152026 Hom.: 50383 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.813 AC: 123691 AN: 152144 Hom.: 50405 Cov.: 32 AF XY: 0.813 AC XY: 60494 AN XY: 74382

African (AFR) AF: 0.745 AC: 30904 AN: 41474

American (AMR) AF: 0.882 AC: 13486 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2814 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4663 AN: 5170

South Asian (SAS) AF: 0.778 AC: 3752 AN: 4822

European-Finnish (FIN) AF: 0.800 AC: 8478 AN: 10594

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56868 AN: 68010

Other (OTH) AF: 0.828 AC: 1748 AN: 2112

Alfa AF: 0.828 Hom.: 158610

Bravo AF: 0.818

Asia WGS AF: 0.811 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.65
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1572237; hg19: chr10-129312691;