Variant chr5-135648666-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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
SLC25A48	NM_001349335.2 linkuse as main transcript	c.-521+13710G>A	intron_variant
SLC25A48	NM_001349345.2 linkuse as main transcript	c.-521+13710G>A	intron_variant
SLC25A48-AS1	NR_027127.1 linkuse as main transcript		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A48-AS1	ENST00000508452.1 linkuse as main transcript	n.2059C>T		non_coding_transcript_exon_variant	3/3	1

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

Gnomad4 NFE exome

AF:

0.300

GnomAD4 genome

AF:

0.276

AC:

41987

AN:

152150

Hom.:

6334

Cov.:

AF XY:

0.281

AC XY:

20920

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.343

Gnomad4 ASJ

AF:

0.194

Gnomad4 EAS

AF:

0.625

Gnomad4 SAS

AF:

0.345

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.268

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.269

Hom.:

2611

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

DANN

Benign

0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over