8-142824280-C-G

Variant names:

• chr8-142824280-C-G
• rs2717594

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 0.472 in 152,046 control chromosomes in the GnomAD database, including 17,280 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 0.47 (17280 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 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: 0.472 AC: 71659 AN: 151928 Hom.: 17245 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.472 AC: 71749 AN: 152046 Hom.: 17280 Cov.: 33 AF XY: 0.475 AC XY: 35261 AN XY: 74306

African (AFR) AF: 0.544 AC: 22535 AN: 41452

American (AMR) AF: 0.479 AC: 7318 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1704 AN: 3466

East Asian (EAS) AF: 0.366 AC: 1894 AN: 5180

South Asian (SAS) AF: 0.464 AC: 2237 AN: 4822

European-Finnish (FIN) AF: 0.461 AC: 4869 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29645 AN: 67964

Other (OTH) AF: 0.482 AC: 1018 AN: 2110

Alfa AF: 0.292 Hom.: 645

Bravo AF: 0.477

Asia WGS AF: 0.412 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.52
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2717594; hg19: chr8-143905696;