rs17040430

Variant names:

• chr12-108349043-G-T
• rs17040430

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;