8-58507880-C-T

Variant names:

• chr8-58507880-C-T
• rs1023650

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 0.527 in 151,628 control chromosomes in the GnomAD database, including 21,836 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 0.53 (21836 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -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 = 0.635 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: 0.527 AC: 79899 AN: 151510 Hom.: 21826 Cov.: 30

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.527 AC: 79929 AN: 151628 Hom.: 21836 Cov.: 30 AF XY: 0.527 AC XY: 39003 AN XY: 74044

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.549

Alfa AF: 0.539 Hom.: 2707

Bravo AF: 0.530

Asia WGS AF: 0.458 AC: 1593 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	6.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023650; hg19: chr8-59420439;