chr9-128111149-A-G

Variant names:

• chr9-128111149-A-G
• rs4837240
• ENST00000418747.2:n.3823T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000418747.2(SLC25A25-AS1):​n.3823T>C 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 0.704 in 152,072 control chromosomes in the GnomAD database, including 40,200 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 0.70 (40198 hom., cov: 32)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: SLC25A25-AS1 ENST00000418747.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418747.2. 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
	SLC25A25-AS1	NR_033374.1		n.*22T>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A25-AS1	ENST00000418747.2	TSL:1	n.3823T>C		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107098 AN: 151948 Hom.: 40196 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.723

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 0.833 AC XY: 5 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.704 AC: 107113 AN: 152066 Hom.: 40198 Cov.: 32 AF XY: 0.704 AC XY: 52328 AN XY: 74318

African (AFR) AF: 0.420 AC: 17390 AN: 41442

American (AMR) AF: 0.739 AC: 11290 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2820 AN: 3464

East Asian (EAS) AF: 0.827 AC: 4287 AN: 5186

South Asian (SAS) AF: 0.718 AC: 3456 AN: 4814

European-Finnish (FIN) AF: 0.817 AC: 8637 AN: 10566

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56745 AN: 67996

Other (OTH) AF: 0.721 AC: 1524 AN: 2114

Alfa AF: 0.789 Hom.: 63216

Bravo AF: 0.687

Asia WGS AF: 0.723 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.9
DANN	Benign	0.87
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4837240; hg19: chr9-130873428;