Genetic Variant ENSG00000293331:n.20+298G>A (chr1-630833-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000452176.2(ENSG00000293331):n.20+298G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000076 in 131,524 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000076 ( 0 hom., cov: 26)

Exomes 𝑓: 0.0000042 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000293331
ENST00000452176.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.584

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293331 (HGNC:):

ENSG00000293331 links:

LINC00115 (HGNC:26211): (long intergenic non-protein coding RNA 115)

LINC00115 links:

MTCO1P12 (HGNC:52014): (MT-CO1 pseudogene 12)

MTCO1P12 links:

MTND2P28 (HGNC:42129): (MT-ND2 pseudogene 28)

MTND2P28 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452176.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000293331	ENST00000452176.2	TSL:1	n.20+298G>A	intron	N/A
LINC00115	ENST00000419394.2	TSL:5	n.481-43878G>A	intron	N/A
ENSG00000293331	ENST00000440196.3	TSL:5	n.87-1827G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00000760

AC:

AN:

131524

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000346

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000425

AC:

AN:

235446

Hom.:

AF XY:

0.00

AC XY:

AN XY:

119596

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

5518

American (AMR)

AF:

0.00

AC:

AN:

7106

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8758

East Asian (EAS)

AF:

0.0000496

AC:

AN:

20146

South Asian (SAS)

AF:

0.00

AC:

AN:

2302

European-Finnish (FIN)

AF:

0.00

AC:

AN:

22796

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1152

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

152226

Other (OTH)

AF:

0.00

AC:

AN:

15442

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.725

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:

0.00000760

AC:

AN:

131524

Hom.:

Cov.:

AF XY:

0.0000156

AC XY:

AN XY:

63912

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0000346

AC:

AN:

28912

American (AMR)

AF:

0.00

AC:

AN:

13728

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3268

East Asian (EAS)

AF:

0.00

AC:

AN:

4662

South Asian (SAS)

AF:

0.00

AC:

AN:

3912

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9444

Middle Eastern (MID)

AF:

0.00

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

64666

Other (OTH)

AF:

0.00

AC:

AN:

1828

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.325

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

3.5

(source)

DANN

Benign

0.75

PhyloP100

0.58

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over