10-129205356-C-G

Variant names:

• chr10-129205356-C-G
• rs1998825

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 0.641 in 151,898 control chromosomes in the GnomAD database, including 31,971 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 0.64 (31971 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.641 AC: 97357 AN: 151782 Hom.: 31965 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.641 AC: 97392 AN: 151898 Hom.: 31971 Cov.: 31 AF XY: 0.643 AC XY: 47733 AN XY: 74232

African (AFR) AF: 0.495 AC: 20503 AN: 41380

American (AMR) AF: 0.693 AC: 10575 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3470

East Asian (EAS) AF: 0.791 AC: 4071 AN: 5144

South Asian (SAS) AF: 0.623 AC: 3001 AN: 4814

European-Finnish (FIN) AF: 0.696 AC: 7346 AN: 10552

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47082 AN: 67952

Other (OTH) AF: 0.657 AC: 1389 AN: 2114

Alfa AF: 0.590 Hom.: 2016

Bravo AF: 0.633

Asia WGS AF: 0.694 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.36
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1998825; hg19: chr10-131003620;