rs12801214

Variant names:

• chr11-44471367-C-T
• rs12801214
• ENST00000528183.2:n.*94C>T

Variant summary

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

The ENST00000528183.2(ENSG00000255451):​n.*94C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0825 in 152,308 control chromosomes in the GnomAD database, including 692 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 0.082 (692 hom., cov: 34)
• Consequence: ENSG00000255451 ENST00000528183.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 3 publications found

Genes affected

ENSG00000255451 (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 (NFE) allele frequency at 95% confidence interval = 0.128 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
ENSG00000255451	ENST00000528183.2	n.*94C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12571 AN: 152190 Hom.: 692 Cov.: 34

Gnomad AFR AF: 0.0253

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0825 AC: 12562 AN: 152308 Hom.: 692 Cov.: 34 AF XY: 0.0789 AC XY: 5877 AN XY: 74460

African (AFR) AF: 0.0252 AC: 1048 AN: 41572

American (AMR) AF: 0.0744 AC: 1139 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 387 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4824

European-Finnish (FIN) AF: 0.0526 AC: 557 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8845 AN: 68024

Other (OTH) AF: 0.0836 AC: 177 AN: 2116

Alfa AF: 0.103 Hom.: 817

Bravo AF: 0.0827

Asia WGS AF: 0.0180 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.58
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs12801214; hg19: chr11-44492917;