rs7017612

Variant names:

• chr8-42744102-A-C
• rs7017612

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;