rs12431733

Variant names:

• chr14-53824112-T-C
• rs12431733
• ENST00000418927.3:n.437+25610A>G

Variant summary

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

The ENST00000418927.3(LINC02331):​n.437+25610A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,112 control chromosomes in the GnomAD database, including 16,241 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 0.45 (16241 hom., cov: 33)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 18 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.289-24334A>G		intron_variant	Intron 2 of 6
LINC02331	NR_184213.1	n.289-24334A>G		intron_variant	Intron 2 of 6
LINC02331	NR_184214.1	n.381+25610A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.3	n.437+25610A>G		intron_variant	Intron 2 of 5	5
DDHD1-DT	ENST00000649040.1	n.66-50392T>C		intron_variant	Intron 1 of 2
DDHD1-DT	ENST00000728781.1	n.177-50392T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68842 AN: 151994 Hom.: 16235 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.453 AC: 68878 AN: 152112 Hom.: 16241 Cov.: 33 AF XY: 0.443 AC XY: 32967 AN XY: 74364

African (AFR) AF: 0.368 AC: 15277 AN: 41502

American (AMR) AF: 0.417 AC: 6376 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.183 AC: 948 AN: 5170

South Asian (SAS) AF: 0.322 AC: 1551 AN: 4816

European-Finnish (FIN) AF: 0.456 AC: 4825 AN: 10584

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36496 AN: 67972

Other (OTH) AF: 0.475 AC: 1003 AN: 2110

Alfa AF: 0.504 Hom.: 91736

Bravo AF: 0.449

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.63
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12431733; hg19: chr14-54290830;