rs9287989

Variant names:

• chr2-175853013-T-C
• rs9287989
• ENST00000840653.1:n.352+20322T>C

Variant summary

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

The ENST00000840653.1(ENSG00000289349):​n.352+20322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,008 control chromosomes in the GnomAD database, including 18,655 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 0.49 (18655 hom., cov: 32)
• Consequence: ENSG00000289349 ENST00000840653.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 9 publications found

Genes affected

ENSG00000289349 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000840653.1	n.352+20322T>C		intron_variant	Intron 3 of 3
ENSG00000289349	ENST00000840654.1	n.499-6025T>C		intron_variant	Intron 2 of 3
ENSG00000289349	ENST00000840655.1	n.326-9498T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74963 AN: 151890 Hom.: 18622 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.494 AC: 75040 AN: 152008 Hom.: 18655 Cov.: 32 AF XY: 0.493 AC XY: 36597 AN XY: 74258

African (AFR) AF: 0.500 AC: 20722 AN: 41484

American (AMR) AF: 0.426 AC: 6502 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3044 AN: 5144

South Asian (SAS) AF: 0.556 AC: 2675 AN: 4814

European-Finnish (FIN) AF: 0.456 AC: 4820 AN: 10566

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33950 AN: 67946

Other (OTH) AF: 0.501 AC: 1059 AN: 2112

Alfa AF: 0.485 Hom.: 6864

Bravo AF: 0.490

Asia WGS AF: 0.593 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9287989; hg19: chr2-176717741;