rs1023652

Variant names:

• chr8-58508057-G-C
• rs1023652

Your query was ambiguous. Multiple possible variants found:

• chr8-58508057-G-C
• chr8-58508057-G-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 0.671 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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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 AC: 0.819364 AN: 0.819364

Gnomad4 AMR AF: 0.727 AC: 0.727374 AN: 0.727374

Gnomad4 ASJ AF: 0.624 AC: 0.623919 AN: 0.623919

Gnomad4 EAS AF: 0.633 AC: 0.632894 AN: 0.632894

Gnomad4 SAS AF: 0.602 AC: 0.601871 AN: 0.601871

Gnomad4 FIN AF: 0.564 AC: 0.564339 AN: 0.564339

Gnomad4 NFE AF: 0.597 AC: 0.596968 AN: 0.596968

Gnomad4 OTH AF: 0.659 AC: 0.659393 AN: 0.659393

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;