Genetic Variant ENSG00000293068:n.51C>T (chr12-4118082-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.574

Publications

2 publications found

Variant links:

Genes affected

ENSG00000293068 (HGNC:):

ENSG00000293068 links:

RPL18P9 (HGNC:36766):

RPL18P9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC124900317	XR_007063172.1 link	n.138C>T	non_coding_transcript_exon_variant	Exon 1 of 5
LOC124900317	XR_007063173.1 link	n.138C>T	non_coding_transcript_exon_variant	Exon 1 of 4
RPL18P9		n.4118082G>A	intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293068	ENST00000393388.3 link	n.51C>T	non_coding_transcript_exon_variant	Exon 1 of 2	3
ENSG00000293068	ENST00000813175.1 link	n.735C>T	non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000293068	ENST00000813176.1 link	n.42C>T	non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

64008

AN:

151892

Hom.:

15339

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.346

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.227

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.422

AC:

64074

AN:

152010

Hom.:

15357

Cov.:

AF XY:

0.425

AC XY:

31599

AN XY:

74314

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1761

3522

5283

7044

8805

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

588

1176

1764

2352

2940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.335

Hom.:

14954

Bravo

AF:

0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.4

(source)

DANN

Benign

0.51

PhyloP100

0.57

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over