rs10505508

Positions:

• chr8-128203678-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 0.204 in 152,146 control chromosomes in the GnomAD database, including 4,414 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 0.20 (4414 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31093 AN: 152028 Hom.: 4416 Cov.: 33

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.204 AC: 31085 AN: 152146 Hom.: 4414 Cov.: 33 AF XY: 0.200 AC XY: 14889 AN XY: 74370

Gnomad4 AFR AF: 0.0486

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.183

Alfa AF: 0.272 Hom.: 3891

Bravo AF: 0.183

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505508; hg19: chr8-129215924;