10-121598798-A-G

Variant names:

• chr10-121598798-A-G
• rs1219639

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 0.868 in 152,226 control chromosomes in the GnomAD database, including 57,853 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 0.87 (57853 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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: 0.868 AC: 132061 AN: 152110 Hom.: 57817 Cov.: 34

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.868 AC: 132155 AN: 152226 Hom.: 57853 Cov.: 34 AF XY: 0.872 AC XY: 64923 AN XY: 74434

African (AFR) AF: 0.740 AC: 30736 AN: 41516

American (AMR) AF: 0.913 AC: 13966 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3224 AN: 3468

East Asian (EAS) AF: 0.972 AC: 5015 AN: 5158

South Asian (SAS) AF: 0.960 AC: 4635 AN: 4826

European-Finnish (FIN) AF: 0.934 AC: 9915 AN: 10616

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61791 AN: 68026

Other (OTH) AF: 0.877 AC: 1848 AN: 2108

Alfa AF: 0.895 Hom.: 79892

Bravo AF: 0.861

Asia WGS AF: 0.953 AC: 3312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.59
PhyloP100		0.22
PromoterAI		0.018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1219639; hg19: chr10-123358312;