rs7017612

Variant names:

• chr8-42744102-A-C
• rs7017612

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.738 AC: 30367 AN: 41172

American (AMR) AF: 0.272 AC: 4092 AN: 15020

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 804 AN: 3286

East Asian (EAS) AF: 0.213 AC: 1104 AN: 5172

South Asian (SAS) AF: 0.254 AC: 1138 AN: 4488

European-Finnish (FIN) AF: 0.187 AC: 1910 AN: 10238

Middle Eastern (MID) AF: 0.241 AC: 66 AN: 274

European-Non Finnish (NFE) AF: 0.188 AC: 12435 AN: 66290

Other (OTH) AF: 0.325 AC: 670 AN: 2062

Alfa AF: 0.226 Hom.: 8521

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7017612; hg19: chr8-42599245;