chr8-128203678-C-T

Variant names:

• chr8-128203678-C-T
• rs10505508

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0486 AC: 2019 AN: 41542

American (AMR) AF: 0.159 AC: 2431 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 758 AN: 3466

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5194

South Asian (SAS) AF: 0.127 AC: 614 AN: 4818

European-Finnish (FIN) AF: 0.322 AC: 3404 AN: 10564

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20999 AN: 67956

Other (OTH) AF: 0.183 AC: 387 AN: 2112

Alfa AF: 0.259 Hom.: 5705

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10505508; hg19: chr8-129215924;