rs7006687

Variant names:

• chr8-18376073-C-T
• rs7006687

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 0.564 in 151,782 control chromosomes in the GnomAD database, including 24,315 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 0.56 (24315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 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: 0.564 AC: 85566 AN: 151666 Hom.: 24288 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.564 AC: 85646 AN: 151782 Hom.: 24315 Cov.: 32 AF XY: 0.563 AC XY: 41752 AN XY: 74188

African (AFR) AF: 0.569 AC: 23538 AN: 41394

American (AMR) AF: 0.580 AC: 8849 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2764 AN: 5150

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4810

European-Finnish (FIN) AF: 0.615 AC: 6486 AN: 10540

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38151 AN: 67860

Other (OTH) AF: 0.549 AC: 1156 AN: 2106

Alfa AF: 0.563 Hom.: 98550

Bravo AF: 0.565

Asia WGS AF: 0.482 AC: 1676 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.40
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7006687; hg19: chr8-18233582;