10-9019407-C-T

Variant names:

• chr10-9019407-C-T
• rs2589559

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 0.762 in 150,570 control chromosomes in the GnomAD database, including 43,801 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 (43801 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.818 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: 0.762 AC: 114606 AN: 150450 Hom.: 43764 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.762 AC: 114704 AN: 150570 Hom.: 43801 Cov.: 31 AF XY: 0.758 AC XY: 55822 AN XY: 73612

African (AFR) AF: 0.661 AC: 26461 AN: 40044

American (AMR) AF: 0.831 AC: 12650 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3033 AN: 3470

East Asian (EAS) AF: 0.799 AC: 4131 AN: 5168

South Asian (SAS) AF: 0.685 AC: 3301 AN: 4816

European-Finnish (FIN) AF: 0.705 AC: 7438 AN: 10552

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55071 AN: 67986

Other (OTH) AF: 0.786 AC: 1652 AN: 2102

Alfa AF: 0.786 Hom.: 18405

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2589559; hg19: chr10-9061370;