rs17040430

Positions:

• chr12-108349043-G-T

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 0.0572 in 152,270 control chromosomes in the GnomAD database, including 279 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 0.057 (279 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.108349043G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0571 AC: 8694 AN: 152152 Hom.: 279 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0538

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0572 AC: 8709 AN: 152270 Hom.: 279 Cov.: 32 AF XY: 0.0551 AC XY: 4101 AN XY: 74460

Gnomad4 AFR AF: 0.0877

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0132

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0538

Gnomad4 OTH AF: 0.0644

Alfa AF: 0.0555 Hom.: 443

Bravo AF: 0.0603

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17040430; hg19: chr12-108742820;