12-4414290-C-T

Variant names:

• chr12-4414290-C-T
• rs10849061

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 0.433 in 151,792 control chromosomes in the GnomAD database, including 15,267 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 0.43 (15267 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 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: 0.433 AC: 65687 AN: 151674 Hom.: 15264 Cov.: 30

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.433 AC: 65711 AN: 151792 Hom.: 15267 Cov.: 30 AF XY: 0.425 AC XY: 31535 AN XY: 74150

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.465

Alfa AF: 0.513 Hom.: 32773

Bravo AF: 0.422

Asia WGS AF: 0.304 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10849061; hg19: chr12-4523456;