chr8-58506952-C-A

Variant names:

• chr8-58506952-C-A
• rs1125226

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 0.538 in 151,910 control chromosomes in the GnomAD database, including 22,603 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 0.54 (22603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 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: 0.539 AC: 81739 AN: 151790 Hom.: 22593 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.538 AC: 81775 AN: 151910 Hom.: 22603 Cov.: 31 AF XY: 0.537 AC XY: 39881 AN XY: 74232

African (AFR) AF: 0.418 AC: 17289 AN: 41408

American (AMR) AF: 0.650 AC: 9920 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2121 AN: 3472

East Asian (EAS) AF: 0.393 AC: 2032 AN: 5174

South Asian (SAS) AF: 0.516 AC: 2485 AN: 4820

European-Finnish (FIN) AF: 0.556 AC: 5851 AN: 10522

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40214 AN: 67932

Other (OTH) AF: 0.555 AC: 1170 AN: 2108

Alfa AF: 0.545 Hom.: 2961

Bravo AF: 0.542

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs1125226; hg19: chr8-59419511;