rs9333284

Variant names:

• chr2-183911704-C-T
• rs9333284
• ENST00000441026.1:n.103+7073C>T

Variant summary

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

The ENST00000441026.1(ENSG00000234172):​n.103+7073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,942 control chromosomes in the GnomAD database, including 9,026 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 0.33 (9026 hom., cov: 33)
• Consequence: ENSG00000234172 ENST00000441026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 0 publications found

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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
ENSG00000234172	ENST00000441026.1	n.103+7073C>T		intron_variant	Intron 1 of 2	2
ENSG00000234172	ENST00000828168.1	n.139+7073C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50598 AN: 151824 Hom.: 9030 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.333 AC: 50617 AN: 151942 Hom.: 9026 Cov.: 33 AF XY: 0.330 AC XY: 24480 AN XY: 74258

African (AFR) AF: 0.215 AC: 8935 AN: 41498

American (AMR) AF: 0.345 AC: 5269 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3035 AN: 5178

South Asian (SAS) AF: 0.303 AC: 1461 AN: 4820

European-Finnish (FIN) AF: 0.335 AC: 3538 AN: 10548

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26027 AN: 67860

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.353 Hom.: 1264

Bravo AF: 0.333

Asia WGS AF: 0.417 AC: 1446 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.16
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9333284; hg19: chr2-184776431;