12-41810035-C-T

Position:

• chr12-41810035-C-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 0.885 in 152,210 control chromosomes in the GnomAD database, including 59,739 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 0.88 (59739 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41810035C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134531 AN: 152092 Hom.: 59677 Cov.: 32

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.885 AC: 134651 AN: 152210 Hom.: 59739 Cov.: 32 AF XY: 0.888 AC XY: 66100 AN XY: 74412

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.854

Gnomad4 OTH AF: 0.882

Alfa AF: 0.863 Hom.: 75290

Bravo AF: 0.889

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1817957; hg19: chr12-42203837;