8-58473360-C-T

Variant names:

• chr8-58473360-C-T
• rs2326077

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 0.695 in 151,972 control chromosomes in the GnomAD database, including 36,872 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 0.69 (36872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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: 0.695 AC: 105525 AN: 151854 Hom.: 36839 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.695 AC: 105609 AN: 151972 Hom.: 36872 Cov.: 31 AF XY: 0.693 AC XY: 51494 AN XY: 74278

African (AFR) AF: 0.754 AC: 31253 AN: 41470

American (AMR) AF: 0.762 AC: 11631 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2393 AN: 3464

East Asian (EAS) AF: 0.781 AC: 4015 AN: 5140

South Asian (SAS) AF: 0.667 AC: 3220 AN: 4826

European-Finnish (FIN) AF: 0.603 AC: 6357 AN: 10548

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44469 AN: 67948

Other (OTH) AF: 0.695 AC: 1466 AN: 2108

Alfa AF: 0.661 Hom.: 57659

Bravo AF: 0.712

Asia WGS AF: 0.722 AC: 2508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.4
DANN	Benign	0.52
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2326077; hg19: chr8-59385919;