chr10-129187873-G-A

Variant names:

• chr10-129187873-G-A
• rs997161

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 0.757 in 152,010 control chromosomes in the GnomAD database, including 43,680 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 0.76 (43680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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: 0.757 AC: 114980 AN: 151892 Hom.: 43655 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.757 AC: 115053 AN: 152010 Hom.: 43680 Cov.: 32 AF XY: 0.754 AC XY: 56062 AN XY: 74310

African (AFR) AF: 0.783 AC: 32450 AN: 41468

American (AMR) AF: 0.761 AC: 11628 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2681 AN: 3472

East Asian (EAS) AF: 0.834 AC: 4303 AN: 5158

South Asian (SAS) AF: 0.713 AC: 3433 AN: 4814

European-Finnish (FIN) AF: 0.673 AC: 7098 AN: 10554

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50842 AN: 67948

Other (OTH) AF: 0.768 AC: 1621 AN: 2112

Alfa AF: 0.755 Hom.: 121300

Bravo AF: 0.763

Asia WGS AF: 0.751 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.88
DANN	Benign	0.19
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs997161; hg19: chr10-130986137;