rs7005189

Variant names:

• chr8-80588421-C-T
• rs7005189

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.13 in 152,188 control chromosomes in the GnomAD database, including 1,777 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 (1777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 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: 0.130 AC: 19809 AN: 152070 Hom.: 1766 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.130 AC: 19829 AN: 152188 Hom.: 1777 Cov.: 32 AF XY: 0.133 AC XY: 9873 AN XY: 74408

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.136

Alfa AF: 0.159 Hom.: 2951

Bravo AF: 0.138

Asia WGS AF: 0.239 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	19
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7005189; hg19: chr8-81500656;