chr8-8598026-A-T

Variant names:

• chr8-8598026-A-T
• rs10503378

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 0.0984 in 152,246 control chromosomes in the GnomAD database, including 1,167 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 (1167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.0984 AC: 14966 AN: 152128 Hom.: 1166 Cov.: 32

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.0984 AC: 14983 AN: 152246 Hom.: 1167 Cov.: 32 AF XY: 0.105 AC XY: 7851 AN XY: 74432

African (AFR) AF: 0.0730 AC: 3032 AN: 41546

American (AMR) AF: 0.225 AC: 3440 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1851 AN: 5174

South Asian (SAS) AF: 0.157 AC: 758 AN: 4816

European-Finnish (FIN) AF: 0.103 AC: 1090 AN: 10610

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0644 AC: 4382 AN: 68008

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0724 Hom.: 75

Bravo AF: 0.111

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10503378; hg19: chr8-8455536;