8-109813089-C-T

Variant names:

• chr8-109813089-C-T
• rs10505128

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0267 in 151,856 control chromosomes in the GnomAD database, including 81 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 0.027 (81 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0267 (4060/151856) while in subpopulation NFE AF = 0.0414 (2810/67832). AF 95% confidence interval is 0.0401. There are 81 homozygotes in GnomAd4. There are 1950 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 81 gene

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: 0.0268 AC: 4061 AN: 151738 Hom.: 81 Cov.: 32

Gnomad AFR AF: 0.00773

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.000390

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0414

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0267 AC: 4060 AN: 151856 Hom.: 81 Cov.: 32 AF XY: 0.0263 AC XY: 1950 AN XY: 74200

African (AFR) AF: 0.00771 AC: 320 AN: 41494

American (AMR) AF: 0.0237 AC: 361 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0188 AC: 65 AN: 3466

East Asian (EAS) AF: 0.000391 AC: 2 AN: 5112

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4818

European-Finnish (FIN) AF: 0.0333 AC: 352 AN: 10584

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0414 AC: 2810 AN: 67832

Other (OTH) AF: 0.0204 AC: 43 AN: 2108

Alfa AF: 0.0336 Hom.: 13

Bravo AF: 0.0249

Asia WGS AF: 0.00549 AC: 20 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.56
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs10505128; hg19: chr8-110825318;