ENST00000418927.3:n.843-14146T>G

Variant names:

• chr14-53700754-A-C
• rs210359
• ENST00000418927.3:n.843-14146T>G

Variant summary

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

The ENST00000418927.3(LINC02331):​n.843-14146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 152,286 control chromosomes in the GnomAD database, including 67,800 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 0.94 (67800 hom., cov: 31)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 10 publications found

Genes affected

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

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

LOC105370504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.768-14146T>G		intron_variant	Intron 6 of 6
LINC02331	NR_184214.1	n.779-14146T>G		intron_variant	Intron 5 of 5
LINC02331	NR_184218.1	n.694-14146T>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.3	n.843-14146T>G		intron_variant	Intron 5 of 5	5
DDHD1-DT	ENST00000648066.2	n.850+13380A>C		intron_variant	Intron 5 of 9
DDHD1-DT	ENST00000663444.2	n.792+13380A>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143458 AN: 152168 Hom.: 67747 Cov.: 31

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.949

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.943 AC: 143569 AN: 152286 Hom.: 67800 Cov.: 31 AF XY: 0.941 AC XY: 70074 AN XY: 74458

African (AFR) AF: 0.986 AC: 40975 AN: 41564

American (AMR) AF: 0.932 AC: 14266 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2999 AN: 3472

East Asian (EAS) AF: 0.785 AC: 4056 AN: 5164

South Asian (SAS) AF: 0.886 AC: 4270 AN: 4822

European-Finnish (FIN) AF: 0.964 AC: 10227 AN: 10612

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63686 AN: 68032

Other (OTH) AF: 0.926 AC: 1957 AN: 2114

Alfa AF: 0.933 Hom.: 208480

Bravo AF: 0.941

Asia WGS AF: 0.871 AC: 3031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs210359; hg19: chr14-54167472;