8-42751043-G-T

Variant names:

• chr8-42751043-G-T
• rs9298629

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 0.342 in 152,078 control chromosomes in the GnomAD database, including 12,413 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 0.34 (12413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.341 AC: 51845 AN: 151960 Hom.: 12368 Cov.: 33

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.342 AC: 51950 AN: 152078 Hom.: 12413 Cov.: 33 AF XY: 0.336 AC XY: 24974 AN XY: 74342

African (AFR) AF: 0.683 AC: 28332 AN: 41502

American (AMR) AF: 0.265 AC: 4047 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3460

East Asian (EAS) AF: 0.214 AC: 1108 AN: 5180

South Asian (SAS) AF: 0.205 AC: 987 AN: 4822

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10562

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13916 AN: 67984

Other (OTH) AF: 0.319 AC: 674 AN: 2112

Alfa AF: 0.261 Hom.: 1302

Bravo AF: 0.364

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.045
DANN	Benign	0.39
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs9298629; hg19: chr8-42606186;