chr8-58789796-G-A

Variant names:

• chr8-58789796-G-A
• rs1526167

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 0.499 in 151,864 control chromosomes in the GnomAD database, including 19,087 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 0.50 (19087 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.499 AC: 75710 AN: 151746 Hom.: 19061 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.499 AC: 75792 AN: 151864 Hom.: 19087 Cov.: 31 AF XY: 0.498 AC XY: 36926 AN XY: 74180

African (AFR) AF: 0.565 AC: 23408 AN: 41422

American (AMR) AF: 0.472 AC: 7220 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1714 AN: 3460

East Asian (EAS) AF: 0.505 AC: 2611 AN: 5166

South Asian (SAS) AF: 0.467 AC: 2247 AN: 4812

European-Finnish (FIN) AF: 0.497 AC: 5201 AN: 10472

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31845 AN: 67926

Other (OTH) AF: 0.484 AC: 1023 AN: 2112

Alfa AF: 0.487 Hom.: 6128

Bravo AF: 0.498

Asia WGS AF: 0.539 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.38
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1526167; hg19: chr8-59702355;