rs7006687

Variant names:

• chr8-18376073-C-T
• rs7006687

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.564 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

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.549

Alfa AF: 0.560 Hom.: 48072

Bravo AF: 0.565

Asia WGS AF: 0.482 AC: 1676 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7006687; hg19: chr8-18233582;