rs2184283

Variant names:

• chr14-20438455-G-C
• rs2184283
• ENST00000553568.1:n.75-51G>C

Your query was ambiguous. Multiple possible variants found:

• chr14-20438455-G-C
• chr14-20438455-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687238.1(ENSG00000291038):​n.338-198G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,950 control chromosomes in the GnomAD database, including 12,034 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 0.39 (12032 hom., cov: 31)
  • Exomes 𝑓: 0.32 (2 hom.)
• Consequence: ENSG00000291038 ENST00000687238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

Genes affected

ENSG00000259162 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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
ENSG00000259162	ENST00000553568.1	n.75-51G>C		intron_variant	Intron 2 of 9	6
ENSG00000291038	ENST00000687238.1	n.338-198G>C		intron_variant	Intron 1 of 7
ENSG00000291038	ENST00000700970.1	n.337+418G>C		intron_variant	Intron 1 of 4
ENSG00000291038	ENST00000555016.1	n.-214G>C		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58568 AN: 151798 Hom.: 12015 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.324 AC: 11 AN: 34 Hom.: 2 Cov.: 0 AF XY: 0.150 AC XY: 3 AN XY: 20

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.386 AC: 58629 AN: 151916 Hom.: 12032 Cov.: 31 AF XY: 0.386 AC XY: 28654 AN XY: 74260

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.369

Alfa AF: 0.188 Hom.: 326

Bravo AF: 0.399

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2184283; hg19: chr14-20906614;