ENST00000438582.2:n.385-9547C>T

Variant names:

• chr9-86478840-C-T
• rs353793
• ENST00000438582.2:n.385-9547C>T

Variant summary

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

The ENST00000438582.2(ENSG00000235819):​n.385-9547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,764 control chromosomes in the GnomAD database, including 24,170 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 (24170 hom., cov: 31)
• Consequence: ENSG00000235819 ENST00000438582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 1 publications found

Genes affected

ENSG00000235819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438582.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235819	ENST00000438582.2	TSL:5	n.385-9547C>T		intron	N/A
	ENSG00000235819	ENST00000657061.1		n.359-9547C>T		intron	N/A
	ENSG00000235819	ENST00000739666.1		n.279-34613C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84044 AN: 151646 Hom.: 24150 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.554 AC: 84100 AN: 151764 Hom.: 24170 Cov.: 31 AF XY: 0.565 AC XY: 41898 AN XY: 74146

African (AFR) AF: 0.472 AC: 19512 AN: 41322

American (AMR) AF: 0.663 AC: 10110 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2083 AN: 3464

East Asian (EAS) AF: 0.911 AC: 4715 AN: 5178

South Asian (SAS) AF: 0.823 AC: 3966 AN: 4818

European-Finnish (FIN) AF: 0.585 AC: 6161 AN: 10536

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35777 AN: 67898

Other (OTH) AF: 0.577 AC: 1205 AN: 2090

Alfa AF: 0.539 Hom.: 2707

Bravo AF: 0.554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.38
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs353793; hg19: chr9-89093755;