10-125447269-T-C

Variant names:

• chr10-125447269-T-C
• rs989507

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 0.743 in 152,042 control chromosomes in the GnomAD database, including 42,603 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 0.74 (42603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112946 AN: 151926 Hom.: 42563 Cov.: 31

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.743 AC: 113040 AN: 152042 Hom.: 42603 Cov.: 31 AF XY: 0.743 AC XY: 55220 AN XY: 74280

African (AFR) AF: 0.617 AC: 25580 AN: 41450

American (AMR) AF: 0.807 AC: 12342 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3472

East Asian (EAS) AF: 0.903 AC: 4649 AN: 5146

South Asian (SAS) AF: 0.775 AC: 3725 AN: 4806

European-Finnish (FIN) AF: 0.722 AC: 7641 AN: 10576

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53701 AN: 67992

Other (OTH) AF: 0.760 AC: 1603 AN: 2108

Alfa AF: 0.769 Hom.: 107888

Bravo AF: 0.745

Asia WGS AF: 0.823 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.71
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs989507; hg19: chr10-127135838;