rs12422552

Variant names:

• chr12-14260997-G-C
• rs12422552
• ENST00000774772.1:n.839G>C

Variant summary

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

The ENST00000774772.1(ENSG00000300868):​n.839G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,106 control chromosomes in the GnomAD database, including 7,388 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 0.30 (7388 hom., cov: 32)
• Consequence: ENSG00000300868 ENST00000774772.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 82 publications found

Genes affected

ENSG00000300868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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
ENSG00000300868	ENST00000774772.1	n.839G>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45969 AN: 151988 Hom.: 7374 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.303 AC: 46021 AN: 152106 Hom.: 7388 Cov.: 32 AF XY: 0.300 AC XY: 22312 AN XY: 74376

African (AFR) AF: 0.412 AC: 17088 AN: 41442

American (AMR) AF: 0.231 AC: 3537 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1144 AN: 3472

East Asian (EAS) AF: 0.283 AC: 1467 AN: 5176

South Asian (SAS) AF: 0.373 AC: 1800 AN: 4826

European-Finnish (FIN) AF: 0.213 AC: 2253 AN: 10584

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17796 AN: 68000

Other (OTH) AF: 0.312 AC: 661 AN: 2116

Alfa AF: 0.273 Hom.: 768

Bravo AF: 0.308

Asia WGS AF: 0.357 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.41
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12422552; hg19: chr12-14413931;