12-3055757-C-T

Variant names:

• chr12-3055757-C-T
• rs12425451
• ENST00000821256.1:n.216-3220C>T

Variant summary

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

The ENST00000821256.1(ENSG00000289980):​n.216-3220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,884 control chromosomes in the GnomAD database, including 28,663 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 0.56 (28663 hom., cov: 30)
• Consequence: ENSG00000289980 ENST00000821256.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 10 publications found

Genes affected

ENSG00000289980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821256.1. 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
	ENSG00000289980	ENST00000821256.1		n.216-3220C>T		intron	N/A
	ENSG00000289980	ENST00000821257.1		n.217-3220C>T		intron	N/A
	ENSG00000289980	ENST00000821258.1		n.418+2888C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84654 AN: 151766 Hom.: 28659 Cov.: 30

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.557 AC: 84658 AN: 151884 Hom.: 28663 Cov.: 30 AF XY: 0.561 AC XY: 41659 AN XY: 74208

African (AFR) AF: 0.152 AC: 6301 AN: 41444

American (AMR) AF: 0.689 AC: 10499 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2334 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4711 AN: 5146

South Asian (SAS) AF: 0.707 AC: 3402 AN: 4812

European-Finnish (FIN) AF: 0.663 AC: 6974 AN: 10522

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.711 AC: 48310 AN: 67934

Other (OTH) AF: 0.601 AC: 1264 AN: 2104

Alfa AF: 0.482 Hom.: 8801

Bravo AF: 0.545

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs12425451; hg19: chr12-3164923;