rs2279989

Variant names:

• chr9-1041524-G-A
• rs2279989
• ENST00000653666.2:n.1028+57C>T

Variant summary

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

The ENST00000653666.2(ENSG00000286684):​n.1028+57C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 152,226 control chromosomes in the GnomAD database, including 333 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 0.063 (333 hom., cov: 33)
• Consequence: ENSG00000286684 ENST00000653666.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 4 publications found

Genes affected

ENSG00000286684 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0815 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
ENSG00000286684	ENST00000653666.2	n.1028+57C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9576 AN: 152108 Hom.: 333 Cov.: 33

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0704

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.0834

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0629 AC: 9570 AN: 152226 Hom.: 333 Cov.: 33 AF XY: 0.0630 AC XY: 4691 AN XY: 74430

African (AFR) AF: 0.0391 AC: 1625 AN: 41534

American (AMR) AF: 0.0320 AC: 489 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0657 AC: 228 AN: 3470

East Asian (EAS) AF: 0.0696 AC: 361 AN: 5184

South Asian (SAS) AF: 0.0884 AC: 426 AN: 4818

European-Finnish (FIN) AF: 0.0834 AC: 884 AN: 10598

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0794 AC: 5399 AN: 68008

Other (OTH) AF: 0.0573 AC: 121 AN: 2110

Alfa AF: 0.0727 Hom.: 727

Bravo AF: 0.0582

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.89
DANN	Benign	0.26
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2279989; hg19: chr9-1041524;