rs927821

chr10-102448042-C-Achr10-102448042-C-Gchr10-102448042-C-T

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 0.849 in 152,058 control chromosomes in the GnomAD database, including 54,990 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 0.85 (54990 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129015 AN: 151940 Hom.: 54939 Cov.: 30

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.849 AC: 129125 AN: 152058 Hom.: 54990 Cov.: 30 AF XY: 0.850 AC XY: 63185 AN XY: 74296

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.829

Alfa AF: 0.824 Hom.: 81936

Bravo AF: 0.856

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs927821; hg19: chr10-104207799;