rs4500065

Variant names:

• chr8-67786150-G-C
• rs4500065

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 0.126 in 152,114 control chromosomes in the GnomAD database, including 1,414 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 0.13 (1414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19239 AN: 151996 Hom.: 1413 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.126 AC: 19235 AN: 152114 Hom.: 1414 Cov.: 32 AF XY: 0.127 AC XY: 9463 AN XY: 74360

African (AFR) AF: 0.0515 AC: 2139 AN: 41532

American (AMR) AF: 0.115 AC: 1752 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5160

South Asian (SAS) AF: 0.187 AC: 900 AN: 4822

European-Finnish (FIN) AF: 0.109 AC: 1157 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11174 AN: 67966

Other (OTH) AF: 0.126 AC: 265 AN: 2108

Alfa AF: 0.146 Hom.: 215

Bravo AF: 0.122

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4500065; hg19: chr8-68698385; COSMIC: COSV69484378;