14-53843879-C-T

Variant names:

• chr14-53843879-C-T
• rs11157980
• ENST00000418927.3:n.437+5843G>A

Variant summary

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

The ENST00000418927.3(LINC02331):​n.437+5843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 151,990 control chromosomes in the GnomAD database, including 1,721 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 0.14 (1721 hom., cov: 32)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• 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 (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.288+5936G>A		intron_variant	Intron 2 of 6
LINC02331	NR_184213.1	n.288+5936G>A		intron_variant	Intron 2 of 6
LINC02331	NR_184214.1	n.381+5843G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.3	n.437+5843G>A		intron_variant	Intron 2 of 5	5
DDHD1-DT	ENST00000649040.1	n.66-30625C>T		intron_variant	Intron 1 of 2
DDHD1-DT	ENST00000728781.1	n.177-30625C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21855 AN: 151872 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.144 AC: 21852 AN: 151990 Hom.: 1721 Cov.: 32 AF XY: 0.148 AC XY: 10985 AN XY: 74280

African (AFR) AF: 0.0708 AC: 2938 AN: 41470

American (AMR) AF: 0.183 AC: 2788 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3466

East Asian (EAS) AF: 0.190 AC: 981 AN: 5166

South Asian (SAS) AF: 0.250 AC: 1202 AN: 4812

European-Finnish (FIN) AF: 0.156 AC: 1642 AN: 10520

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11248 AN: 67974

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.152 Hom.: 1107

Bravo AF: 0.141

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.50
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs11157980; hg19: chr14-54310597;