12-121102543-C-T

Variant names:

• chr12-121102543-C-T
• rs1796421
• ENST00000837362.1:n.128-1814G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000837362.1(ENSG00000308932):​n.128-1814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 151,688 control chromosomes in the GnomAD database, including 45,956 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 0.78 (45956 hom., cov: 32)
• Consequence: ENSG00000308932 ENST00000837362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 2 publications found

Genes affected

ENSG00000308932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837362.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308932	ENST00000837362.1		n.128-1814G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117678 AN: 151570 Hom.: 45929 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.776 AC: 117753 AN: 151688 Hom.: 45956 Cov.: 32 AF XY: 0.777 AC XY: 57588 AN XY: 74096

African (AFR) AF: 0.732 AC: 30276 AN: 41352

American (AMR) AF: 0.838 AC: 12768 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2857 AN: 3468

East Asian (EAS) AF: 0.880 AC: 4541 AN: 5162

South Asian (SAS) AF: 0.739 AC: 3563 AN: 4822

European-Finnish (FIN) AF: 0.730 AC: 7636 AN: 10466

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53460 AN: 67880

Other (OTH) AF: 0.788 AC: 1659 AN: 2104

Alfa AF: 0.790 Hom.: 36553

Bravo AF: 0.785

Asia WGS AF: 0.808 AC: 2809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.53
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1796421; hg19: chr12-121540346;