chr8-114894998-T-C

Variant names:

• chr8-114894998-T-C
• rs10505239

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 0.506 in 151,776 control chromosomes in the GnomAD database, including 23,393 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 0.51 (23393 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 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: 0.506 AC: 76739 AN: 151658 Hom.: 23344 Cov.: 30

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.506 AC: 76836 AN: 151776 Hom.: 23393 Cov.: 30 AF XY: 0.504 AC XY: 37356 AN XY: 74192

African (AFR) AF: 0.874 AC: 36152 AN: 41382

American (AMR) AF: 0.365 AC: 5572 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1212 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1633 AN: 5132

South Asian (SAS) AF: 0.423 AC: 2029 AN: 4798

European-Finnish (FIN) AF: 0.388 AC: 4081 AN: 10522

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24892 AN: 67910

Other (OTH) AF: 0.433 AC: 912 AN: 2108

Alfa AF: 0.427 Hom.: 5271

Bravo AF: 0.513

Asia WGS AF: 0.397 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.53
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs10505239; hg19: chr8-115907227;