12-41741966-A-G

Position:

• chr12-41741966-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 0.651 in 151,482 control chromosomes in the GnomAD database, including 32,577 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 0.65 (32577 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41741966A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98607 AN: 151364 Hom.: 32554 Cov.: 29

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.651 AC: 98670 AN: 151482 Hom.: 32577 Cov.: 29 AF XY: 0.653 AC XY: 48329 AN XY: 73982

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.664

Alfa AF: 0.645 Hom.: 39620

Bravo AF: 0.660

Asia WGS AF: 0.786 AC: 2730 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220999; hg19: chr12-42135768;