dbSNP rs801564: SLC25A48-AS1:n.2059C>T (chr5-135648666-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 ENST00000508452.1(SLC25A48-AS1):n.2059C>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 0.276 in 152,160 control chromosomes in the GnomAD database, including 6,334 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 0.28 ( 6334 hom., cov: 33)

Exomes 𝑓: 0.30 ( 0 hom. )

Consequence

SLC25A48-AS1
ENST00000508452.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.191

Publications

5 publications found

Variant links:

Genes affected

SLC25A48-AS1 (HGNC:27965): (SLC25A48 antisense RNA 1)

SLC25A48-AS1 links:

SLC25A48 (HGNC:30451): (solute carrier family 25 member 48) Predicted to enable acyl carnitine transmembrane transporter activity. Predicted to be involved in acyl carnitine transport and amino acid transport. Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC25A48 links:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
SLC25A48	NM_001349335.2 link	c.-521+13710G>A	intron_variant	Intron 3 of 10	NP_001336264.1
SLC25A48	NM_001349345.2 link	c.-521+13710G>A	intron_variant	Intron 3 of 9	NP_001336274.1
SLC25A48-AS1	NR_027127.1 link	n.*17C>T	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SLC25A48-AS1	ENST00000508452.1 link	n.2059C>T	non_coding_transcript_exon_variant	Exon 3 of 3	1
SLC25A48	ENST00000646290.1 link	c.-521+13710G>A	intron_variant	Intron 3 of 10		ENSP00000493514.1	J3KQI1
SLC25A48	ENST00000647391.1 link	n.745+13710G>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

41939

AN:

152032

Hom.:

6322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.626

Gnomad SAS

AF:

0.344

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.282

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

Cov.:

AF XY:

0.300

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

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:

0.300

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.392

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.276

AC:

41987

AN:

152150

Hom.:

6334

Cov.:

AF XY:

0.281

AC XY:

20920

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.215

AC:

8911

AN:

41510

American (AMR)

AF:

0.343

AC:

5249

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

673

AN:

3468

East Asian (EAS)

AF:

0.625

AC:

3233

AN:

5170

South Asian (SAS)

AF:

0.345

AC:

1664

AN:

4824

European-Finnish (FIN)

AF:

0.310

AC:

3277

AN:

10576

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.268

AC:

18202

AN:

67994

Other (OTH)

AF:

0.288

AC:

607

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1541

3082

4624

6165

7706

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.267

Hom.:

2909

Bravo

AF:

0.279

Asia WGS

AF:

0.456

AC:

1582

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.5

(source)

DANN

Benign

0.74

PhyloP100

0.19

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over