14-85388811-A-G

Variant names:

• chr14-85388811-A-G
• rs1885316
• ENST00000557547.1:n.357+9338T>C

Variant summary

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

The ENST00000557547.1(ENSG00000258902):​n.357+9338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,888 control chromosomes in the GnomAD database, including 22,437 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 0.53 (22437 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000258902 ENST00000557547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

ENSG00000258902 (HGNC:):

LINC02329 (HGNC:53249): (long intergenic non-protein coding RNA 2329)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02329	NR_135155.1	n.*46A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258902	ENST00000557547.1	n.357+9338T>C		intron_variant	Intron 3 of 4	4
LINC02329	ENST00000554753.2	n.*46A>G		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80554 AN: 151770 Hom.: 22391 Cov.: 33

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.505

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.531 AC: 80654 AN: 151888 Hom.: 22437 Cov.: 33 AF XY: 0.524 AC XY: 38892 AN XY: 74252

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.501

Alfa AF: 0.467 Hom.: 8480

Bravo AF: 0.539

Asia WGS AF: 0.392 AC: 1362 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885316; hg19: chr14-85855155;