8-58795750-C-T

Variant names:

• chr8-58795750-C-T
• rs960089

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 0.0975 in 150,816 control chromosomes in the GnomAD database, including 893 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 0.098 (893 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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: 0.0974 AC: 14683 AN: 150700 Hom.: 891 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0659

Gnomad EAS AF: 0.00702

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0792

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

GnomAD4 genome AF: 0.0975 AC: 14712 AN: 150816 Hom.: 893 Cov.: 31 AF XY: 0.0982 AC XY: 7225 AN XY: 73570

African (AFR) AF: 0.153 AC: 6258 AN: 41008

American (AMR) AF: 0.0601 AC: 905 AN: 15066

Ashkenazi Jewish (ASJ) AF: 0.0659 AC: 228 AN: 3460

East Asian (EAS) AF: 0.00724 AC: 37 AN: 5114

South Asian (SAS) AF: 0.0522 AC: 249 AN: 4770

European-Finnish (FIN) AF: 0.131 AC: 1358 AN: 10350

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0804 AC: 5445 AN: 67748

Other (OTH) AF: 0.0831 AC: 174 AN: 2094

Alfa AF: 0.0815 Hom.: 2366

Bravo AF: 0.0941

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.66
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs960089; hg19: chr8-59708309;