rs7006896

Variant names:

• chr8-129809948-G-A
• rs7006896

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 0.132 in 152,176 control chromosomes in the GnomAD database, including 1,510 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 (1510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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: 0.132 AC: 20092 AN: 152058 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.132 AC: 20086 AN: 152176 Hom.: 1510 Cov.: 32 AF XY: 0.132 AC XY: 9801 AN XY: 74388

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.166

Alfa AF: 0.143 Hom.: 216

Bravo AF: 0.129

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7006896; hg19: chr8-130822194;