ENST00000393388.3:n.51C>T

Variant names:

• chr12-4118082-G-A
• rs741245
• ENST00000393388.3:n.51C>T

Variant summary

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

The ENST00000393388.3(ENSG00000293068):​n.51C>T 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 0.421 in 152,042 control chromosomes in the GnomAD database, including 15,360 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 0.42 (15357 hom., cov: 32)
  • Exomes 𝑓: 0.28 (3 hom.)
• Consequence: ENSG00000293068 ENST00000393388.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574
• Publications: 2 publications found

Genes affected

ENSG00000293068 (HGNC:):

RPL18P9 (HGNC:36766):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000393388.3. 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
	ENSG00000293068	ENST00000393388.3	TSL:3	n.51C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000293068	ENST00000813175.1		n.735C>T		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000293068	ENST00000813176.1		n.42C>T		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64008 AN: 151892 Hom.: 15339 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.414

GnomAD4 exome AF: 0.281 AC: 9 AN: 32 Hom.: 3 Cov.: 0 AF XY: 0.346 AC XY: 9 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.227 AC: 5 AN: 22

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.422 AC: 64074 AN: 152010 Hom.: 15357 Cov.: 32 AF XY: 0.425 AC XY: 31599 AN XY: 74314

African (AFR) AF: 0.602 AC: 24976 AN: 41460

American (AMR) AF: 0.413 AC: 6319 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3468

East Asian (EAS) AF: 0.840 AC: 4337 AN: 5164

South Asian (SAS) AF: 0.496 AC: 2389 AN: 4814

European-Finnish (FIN) AF: 0.288 AC: 3041 AN: 10562

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20579 AN: 67944

Other (OTH) AF: 0.411 AC: 867 AN: 2112

Alfa AF: 0.335 Hom.: 14954

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs741245;

hg19: chr12-4227248;