14-53725754-C-T

Variant names:

• chr14-53725754-C-T
• rs210332
• ENST00000418927.3:n.842+24248G>A

Variant summary

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

The ENST00000418927.3(LINC02331):​n.842+24248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,830 control chromosomes in the GnomAD database, including 46,609 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 0.78 (46609 hom., cov: 29)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418927.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02331	NR_184212.1		n.767+24248G>A		intron	N/A
	LINC02331	NR_184213.1		n.768-22600G>A		intron	N/A
	LINC02331	NR_184214.1		n.778+24248G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02331	ENST00000418927.3	TSL:5	n.842+24248G>A		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.851-11913C>T		intron	N/A
	DDHD1-DT	ENST00000728781.1		n.176+38380C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118779 AN: 151712 Hom.: 46584 Cov.: 29

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.783 AC: 118859 AN: 151830 Hom.: 46609 Cov.: 29 AF XY: 0.781 AC XY: 57989 AN XY: 74206

African (AFR) AF: 0.733 AC: 30296 AN: 41344

American (AMR) AF: 0.825 AC: 12595 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3049 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4150 AN: 5142

South Asian (SAS) AF: 0.709 AC: 3409 AN: 4808

European-Finnish (FIN) AF: 0.807 AC: 8509 AN: 10542

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54122 AN: 67952

Other (OTH) AF: 0.817 AC: 1721 AN: 2106

Alfa AF: 0.798 Hom.: 98834

Bravo AF: 0.786

Asia WGS AF: 0.740 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs210332; hg19: chr14-54192472;