8-65083360-T-G

Variant names:

• chr8-65083360-T-G
• rs10504382

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 0.161 in 152,054 control chromosomes in the GnomAD database, including 2,377 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 0.16 (2377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 4 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 = 0.451 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24510 AN: 151936 Hom.: 2381 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.161 AC: 24522 AN: 152054 Hom.: 2377 Cov.: 32 AF XY: 0.170 AC XY: 12653 AN XY: 74318

African (AFR) AF: 0.128 AC: 5299 AN: 41484

American (AMR) AF: 0.190 AC: 2900 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2410 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1086 AN: 4806

European-Finnish (FIN) AF: 0.249 AC: 2626 AN: 10556

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9414 AN: 67996

Other (OTH) AF: 0.131 AC: 276 AN: 2110

Alfa AF: 0.146 Hom.: 7041

Bravo AF: 0.157

Asia WGS AF: 0.283 AC: 981 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.69
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10504382; hg19: chr8-65995595;