8-15259029-G-C

Variant names:

• chr8-15259029-G-C
• rs7818744

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 0.479 in 152,046 control chromosomes in the GnomAD database, including 19,602 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 0.48 (19602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72721 AN: 151928 Hom.: 19547 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.479 AC: 72830 AN: 152046 Hom.: 19602 Cov.: 32 AF XY: 0.475 AC XY: 35342 AN XY: 74332

African (AFR) AF: 0.731 AC: 30339 AN: 41504

American (AMR) AF: 0.482 AC: 7369 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1788 AN: 5154

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4822

European-Finnish (FIN) AF: 0.257 AC: 2715 AN: 10568

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.374 AC: 25414 AN: 67940

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.426 Hom.: 1950

Bravo AF: 0.503

Asia WGS AF: 0.436 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.82
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs7818744; hg19: chr8-15116538;