rs17037068

Positions:

• chr12-105415167-C-G

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 0.0619 in 152,230 control chromosomes in the GnomAD database, including 763 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 0.062 (763 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105415167C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0618 AC: 9403 AN: 152112 Hom.: 761 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0267

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00615

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.00377

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0619 AC: 9424 AN: 152230 Hom.: 763 Cov.: 33 AF XY: 0.0592 AC XY: 4408 AN XY: 74434

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0266

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.00617

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.00377

Gnomad4 NFE AF: 0.0125

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0409 Hom.: 63

Bravo AF: 0.0693

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17037068; hg19: chr12-105808945;