rs1023651

Variant names:

• chr8-58507952-C-A
• rs1023651

Your query was ambiguous. Multiple possible variants found:

• chr8-58507952-C-A
• chr8-58507952-C-T

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 0.539 in 151,780 control chromosomes in the GnomAD database, including 22,591 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 (22591 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81695 AN: 151662 Hom.: 22578 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.539 AC: 81737 AN: 151780 Hom.: 22591 Cov.: 31 AF XY: 0.537 AC XY: 39828 AN XY: 74136

African (AFR) AF: 0.418 AC: 17273 AN: 41326

American (AMR) AF: 0.650 AC: 9912 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2034 AN: 5164

South Asian (SAS) AF: 0.515 AC: 2486 AN: 4828

European-Finnish (FIN) AF: 0.556 AC: 5840 AN: 10498

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

European-Non Finnish (NFE) AF: 0.592 AC: 40213 AN: 67932

Other (OTH) AF: 0.555 AC: 1169 AN: 2108

Alfa AF: 0.409 Hom.: 1134

Bravo AF: 0.542

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.98
DANN	Benign	0.78
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1023651; hg19: chr8-59420511;