9-93323088-C-T

Variant names:

• chr9-93323088-C-T
• rs3001450
• ENST00000648864.2:n.730-3914G>A

Variant summary

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

The ENST00000648864.2(ENSG00000290685):​n.730-3914G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 121,666 control chromosomes in the GnomAD database, including 13,561 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 0.48 (13561 hom., cov: 32)
• Consequence: ENSG00000290685 ENST00000648864.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 5 publications found

Genes affected

ENSG00000290685 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648864.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290685	ENST00000648864.2		n.730-3914G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.476 AC: 57864 AN: 121580 Hom.: 13558 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.476 AC: 57862 AN: 121666 Hom.: 13561 Cov.: 32 AF XY: 0.476 AC XY: 27975 AN XY: 58766

African (AFR) AF: 0.154 AC: 4235 AN: 27464

American (AMR) AF: 0.594 AC: 7748 AN: 13044

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1364 AN: 2812

East Asian (EAS) AF: 0.530 AC: 2141 AN: 4042

South Asian (SAS) AF: 0.423 AC: 1247 AN: 2948

European-Finnish (FIN) AF: 0.561 AC: 4780 AN: 8514

Middle Eastern (MID) AF: 0.359 AC: 84 AN: 234

European-Non Finnish (NFE) AF: 0.582 AC: 35080 AN: 60234

Other (OTH) AF: 0.485 AC: 786 AN: 1620

Alfa AF: 0.457 Hom.: 3022

Bravo AF: 0.380

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3001450; hg19: chr9-96085370;