10-22029172-T-C

Variant names:

• chr10-22029172-T-C
• rs4529807

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 0.827 in 152,206 control chromosomes in the GnomAD database, including 52,663 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 0.83 (52663 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.941 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: 0.827 AC: 125845 AN: 152088 Hom.: 52617 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.827 AC: 125943 AN: 152206 Hom.: 52663 Cov.: 31 AF XY: 0.830 AC XY: 61773 AN XY: 74416

African (AFR) AF: 0.949 AC: 39433 AN: 41542

American (AMR) AF: 0.766 AC: 11691 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2522 AN: 3472

East Asian (EAS) AF: 0.947 AC: 4899 AN: 5174

South Asian (SAS) AF: 0.856 AC: 4129 AN: 4826

European-Finnish (FIN) AF: 0.836 AC: 8861 AN: 10602

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51880 AN: 68008

Other (OTH) AF: 0.816 AC: 1721 AN: 2110

Alfa AF: 0.782 Hom.: 57750

Bravo AF: 0.827

Asia WGS AF: 0.857 AC: 2980 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	1.2
DANN	Benign	0.79
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4529807; hg19: chr10-22318101;