rs62514004

Variant names:

• chr8-133190246-A-G
• rs62514004

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 0.277 in 151,976 control chromosomes in the GnomAD database, including 6,614 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 0.28 (6614 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 13 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 (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42070 AN: 151858 Hom.: 6617 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.277 AC: 42079 AN: 151976 Hom.: 6614 Cov.: 31 AF XY: 0.280 AC XY: 20779 AN XY: 74256

African (AFR) AF: 0.163 AC: 6753 AN: 41470

American (AMR) AF: 0.227 AC: 3470 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1004 AN: 3472

East Asian (EAS) AF: 0.122 AC: 628 AN: 5168

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4824

European-Finnish (FIN) AF: 0.422 AC: 4448 AN: 10538

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23393 AN: 67932

Other (OTH) AF: 0.253 AC: 532 AN: 2106

Alfa AF: 0.309 Hom.: 3102

Bravo AF: 0.253

Asia WGS AF: 0.204 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs62514004; hg19: chr8-134202489;