10-9019407-C-T

Variant names:

• chr10-9019407-C-T
• rs2589559

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.786

Alfa AF: 0.781 Hom.: 10224

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2589559; hg19: chr10-9061370;