14-53781365-C-T

Variant names:

• chr14-53781365-C-T
• rs17126895
• ENST00000418927.3:n.580+11889G>A

Variant summary

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

The ENST00000418927.3(LINC02331):​n.580+11889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,892 control chromosomes in the GnomAD database, including 3,535 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 0.21 (3535 hom., cov: 32)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 5 publications found

Genes affected

LINC02331 (HGNC:53251): (long intergenic non-protein coding RNA 2331)

DDHD1-DT (HGNC:55441): (DDHD1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.505+11889G>A		intron_variant	Intron 4 of 6
LINC02331	NR_184213.1	n.505+11889G>A		intron_variant	Intron 4 of 6
LINC02331	NR_184214.1	n.524+11889G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.3	n.580+11889G>A		intron_variant	Intron 3 of 5	5
DDHD1-DT	ENST00000648066.2	n.1132-3780C>T		intron_variant	Intron 8 of 9
DDHD1-DT	ENST00000649040.1	n.65+15646C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32052 AN: 151772 Hom.: 3533 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.211 AC: 32070 AN: 151892 Hom.: 3535 Cov.: 32 AF XY: 0.219 AC XY: 16279 AN XY: 74190

African (AFR) AF: 0.183 AC: 7570 AN: 41432

American (AMR) AF: 0.201 AC: 3067 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2110 AN: 5154

South Asian (SAS) AF: 0.328 AC: 1574 AN: 4794

European-Finnish (FIN) AF: 0.279 AC: 2934 AN: 10520

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13469 AN: 67948

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.198 Hom.: 5571

Bravo AF: 0.202

Asia WGS AF: 0.324 AC: 1120 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs17126895; hg19: chr14-54248083;