Genetic Variant SLC25A25-AS1:n.144C>T (chr9-128118550-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 ENST00000418747.2(SLC25A25-AS1):n.144C>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 0.822 in 152,264 control chromosomes in the GnomAD database, including 52,010 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 0.82 ( 51897 hom., cov: 30)

Exomes 𝑓: 0.88 ( 113 hom. )

Consequence

SLC25A25-AS1
ENST00000418747.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.435

Publications

7 publications found

Variant links:

Genes affected

SLC25A25-AS1 (HGNC:27844): (SLC25A25 antisense RNA 1)

SLC25A25-AS1 links:

ENSG00000297862 (HGNC:):

ENSG00000297862 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A25-AS1	NR_033374.1 link	n.185C>T		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SLC25A25-AS1	ENST00000418747.2 link	n.144C>T	non_coding_transcript_exon_variant	Exon 1 of 5	1
ENSG00000297862	ENST00000751429.1 link	n.236+106G>A	intron_variant	Intron 2 of 2
ENSG00000297862	ENST00000751430.1 link	n.243+106G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.822

AC:

124874

AN:

151854

Hom.:

51870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.708

Gnomad AMI

AF:

0.826

Gnomad AMR

AF:

0.814

Gnomad ASJ

AF:

0.816

Gnomad EAS

AF:

0.899

Gnomad SAS

AF:

0.804

Gnomad FIN

AF:

0.909

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.876

Gnomad OTH

AF:

0.815

GnomAD4 exome

AF:

0.877

AC:

256

AN:

292

Hom.:

113

Cov.:

AF XY:

0.868

AC XY:

165

AN XY:

190

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.700

AC:

AN:

European-Finnish (FIN)

AF:

0.878

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.882

AC:

150

AN:

170

Other (OTH)

AF:

0.882

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.822

AC:

124953

AN:

151972

Hom.:

51897

Cov.:

AF XY:

0.823

AC XY:

61093

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.708

AC:

29310

AN:

41392

American (AMR)

AF:

0.814

AC:

12433

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.816

AC:

2832

AN:

3472

East Asian (EAS)

AF:

0.899

AC:

4621

AN:

5140

South Asian (SAS)

AF:

0.804

AC:

3874

AN:

4816

European-Finnish (FIN)

AF:

0.909

AC:

9621

AN:

10586

Middle Eastern (MID)

AF:

0.779

AC:

229

AN:

294

European-Non Finnish (NFE)

AF:

0.876

AC:

59559

AN:

67970

Other (OTH)

AF:

0.814

AC:

1721

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1057

2114

3170

4227

5284

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

880

1760

2640

3520

4400

<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:

0.803

Hom.:

3802

Bravo

AF:

0.812

Asia WGS

AF:

0.824

AC:

2866

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

0.68

(source)

DANN

Benign

0.51

PhyloP100

-0.43

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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