chr12-108349043-G-T

Variant names:

• chr12-108349043-G-T
• rs17040430

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 0.0572 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0877 AC: 3641 AN: 41538

American (AMR) AF: 0.0434 AC: 664 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.00173 AC: 9 AN: 5194

South Asian (SAS) AF: 0.0132 AC: 64 AN: 4834

European-Finnish (FIN) AF: 0.0352 AC: 374 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0538 AC: 3659 AN: 68008

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

Alfa AF: 0.0556 Hom.: 1030

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
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs17040430; hg19: chr12-108742820;