rs7006687

Positions:

• chr8-18376073-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;