rs1023652

chr8-58508057-G-Cchr8-58508057-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.671 in 151,958 control chromosomes in the GnomAD database, including 34,950 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 0.67 (34950 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101902 AN: 151840 Hom.: 34908 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.671 AC: 102000 AN: 151958 Hom.: 34950 Cov.: 31 AF XY: 0.669 AC XY: 49673 AN XY: 74248

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.659

Alfa AF: 0.468 Hom.: 1104

Bravo AF: 0.691

Asia WGS AF: 0.625 AC: 2173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.8
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023652; hg19: chr8-59420616;