rs10504255

chr8-58485902-G-Achr8-58485902-G-Cchr8-58485902-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.745 in 152,144 control chromosomes in the GnomAD database, including 43,272 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 0.75 (43272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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: 0.745 AC: 113229 AN: 152026 Hom.: 43208 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.745 AC: 113355 AN: 152144 Hom.: 43272 Cov.: 32 AF XY: 0.742 AC XY: 55184 AN XY: 74352

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.732

Alfa AF: 0.672 Hom.: 46148

Bravo AF: 0.766

Asia WGS AF: 0.742 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	12
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504255; hg19: chr8-59398461;