8-58507880-C-T

Position:

• chr8-58507880-C-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 0.527 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;