10-121598798-A-G

Variant names:

• chr10-121598798-A-G
• rs1219639

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 0.868 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.868 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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.877

Alfa AF: 0.900 Hom.: 55147

Bravo AF: 0.861

Asia WGS AF: 0.953 AC: 3312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1219639; hg19: chr10-123358312;