9-128118550-G-A

Position:

• chr9-128118550-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033374.1(SLC25A25-AS1):​n.185C>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 NR_033374.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC25A25-AS1	NR_033374.1	n.185C>T		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A25-AS1	ENST00000418747.2	n.144C>T		non_coding_transcript_exon_variant	1/5	1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124874 AN: 151854 Hom.: 51870 Cov.: 30

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.: 0 AF XY: 0.868 AC XY: 165 AN XY: 190

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.700

Gnomad4 FIN exome AF: 0.878

Gnomad4 NFE exome AF: 0.882

Gnomad4 OTH exome AF: 0.882

GnomAD4 genome AF: 0.822 AC: 124953 AN: 151972 Hom.: 51897 Cov.: 30 AF XY: 0.823 AC XY: 61093 AN XY: 74254

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.814

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
DANN	Benign	0.51
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

LitVar

Other links and lift over

dbSNP: rs10987883; hg19: chr9-130880829;