rs7017612

chr8-42744102-A-C

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 0.354 in 148,864 control chromosomes in the GnomAD database, including 14,145 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 0.35 (14145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.354 AC: 52602 AN: 148738 Hom.: 14099 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.354 AC: 52705 AN: 148864 Hom.: 14145 Cov.: 31 AF XY: 0.348 AC XY: 25306 AN XY: 72750

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.325

Alfa AF: 0.206 Hom.: 5430

Bravo AF: 0.388

Asia WGS AF: 0.297 AC: 1031 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.9
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7017612; hg19: chr8-42599245;