rs789254

Variant names:

• chr3-128855750-C-T
• rs789254
• ENST00000498297.3:n.3321G>A

Variant summary

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

The ENST00000498297.3(ACAD9-DT):​n.3321G>A 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 0.554 in 152,100 control chromosomes in the GnomAD database, including 26,426 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 0.55 (26426 hom., cov: 32)
• Consequence: ACAD9-DT ENST00000498297.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 4 publications found

Genes affected

ACAD9-DT (HGNC:56086): (ACAD9 divergent transcript)

ENSG00000290241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498297.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACAD9-DT	ENST00000498297.3	TSL:3	n.3321G>A		non_coding_transcript_exon	Exon 6 of 6
	ENSG00000290241	ENST00000703685.1		n.437+4774C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84217 AN: 151982 Hom.: 26423 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.568

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.554 AC: 84241 AN: 152100 Hom.: 26426 Cov.: 32 AF XY: 0.558 AC XY: 41499 AN XY: 74368

African (AFR) AF: 0.247 AC: 10263 AN: 41474

American (AMR) AF: 0.596 AC: 9109 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2080 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1996 AN: 5182

South Asian (SAS) AF: 0.616 AC: 2967 AN: 4818

European-Finnish (FIN) AF: 0.725 AC: 7663 AN: 10576

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48054 AN: 67984

Other (OTH) AF: 0.569 AC: 1199 AN: 2108

Alfa AF: 0.613 Hom.: 5366

Bravo AF: 0.529

Asia WGS AF: 0.523 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.39
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs789254; hg19: chr3-128574593;