14-85388811-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000258902 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557547.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02329	NR_135155.1		n.*46A>G		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258902	ENST00000557547.1	TSL:4	n.357+9338T>C		intron	N/A
	LINC02329	ENST00000554753.2	TSL:5	n.*46A>G		downstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.714 AC: 29586 AN: 41446

American (AMR) AF: 0.463 AC: 7053 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1750 AN: 3464

East Asian (EAS) AF: 0.253 AC: 1311 AN: 5182

South Asian (SAS) AF: 0.484 AC: 2339 AN: 4828

European-Finnish (FIN) AF: 0.434 AC: 4580 AN: 10550

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32340 AN: 67878

Other (OTH) AF: 0.501 AC: 1058 AN: 2110

Alfa AF: 0.470 Hom.: 9405

Bravo AF: 0.539

Asia WGS AF: 0.392 AC: 1362 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.36
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1885316; hg19: chr14-85855155;