rs2818309

Variant names:

• chr9-118977520-C-T
• rs2818309
• ENST00000785114.1:n.175-29066G>A

Variant summary

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

The ENST00000785114.1(ENSG00000302233):​n.175-29066G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,826 control chromosomes in the GnomAD database, including 27,956 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 0.59 (27956 hom., cov: 32)
• Consequence: ENSG00000302233 ENST00000785114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 3 publications found

Genes affected

ENSG00000302233 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928849	XR_001746918.2	n.1046+84C>T		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302233	ENST00000785114.1	n.175-29066G>A		intron_variant	Intron 1 of 1
ENSG00000302233	ENST00000785115.1	n.138-29066G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89671 AN: 151708 Hom.: 27952 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.591 AC: 89689 AN: 151826 Hom.: 27956 Cov.: 32 AF XY: 0.591 AC XY: 43838 AN XY: 74220

African (AFR) AF: 0.381 AC: 15772 AN: 41408

American (AMR) AF: 0.695 AC: 10582 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3110 AN: 5166

South Asian (SAS) AF: 0.495 AC: 2383 AN: 4818

European-Finnish (FIN) AF: 0.651 AC: 6885 AN: 10568

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.689 AC: 46747 AN: 67868

Other (OTH) AF: 0.578 AC: 1219 AN: 2110

Alfa AF: 0.639 Hom.: 5622

Bravo AF: 0.594

Asia WGS AF: 0.563 AC: 1960 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs2818309; hg19: chr9-121739798;