chr12-41129907-A-G

Position:

• chr12-41129907-A-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 0.475 in 151,668 control chromosomes in the GnomAD database, including 17,498 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 0.48 (17498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72013 AN: 151550 Hom.: 17477 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.475 AC: 72079 AN: 151668 Hom.: 17498 Cov.: 32 AF XY: 0.475 AC XY: 35205 AN XY: 74124

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.452

Alfa AF: 0.451 Hom.: 4805

Bravo AF: 0.474

Asia WGS AF: 0.391 AC: 1361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726402; hg19: chr12-41523709;