rs8017615

Variant names:

• chr14-53792880-T-C
• rs8017615
• ENST00000418927.3:n.580+374A>G

Variant summary

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

The NR_184212.1(LINC02331):​n.505+374A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 152,106 control chromosomes in the GnomAD database, including 196 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 0.042 (196 hom., cov: 31)
• Consequence: LINC02331 NR_184212.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0899 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_184212.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02331	NR_184212.1		n.505+374A>G		intron	N/A
	LINC02331	NR_184213.1		n.505+374A>G		intron	N/A
	LINC02331	NR_184214.1		n.524+374A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02331	ENST00000418927.3	TSL:5	n.580+374A>G		intron	N/A
	DDHD1-DT	ENST00000649040.1		n.65+27161T>C		intron	N/A
	DDHD1-DT	ENST00000728781.1		n.177-81624T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6370 AN: 151988 Hom.: 196 Cov.: 31

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.0623

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

GnomAD4 genome AF: 0.0419 AC: 6366 AN: 152106 Hom.: 196 Cov.: 31 AF XY: 0.0419 AC XY: 3118 AN XY: 74350

African (AFR) AF: 0.0106 AC: 441 AN: 41514

American (AMR) AF: 0.0412 AC: 629 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.0969 AC: 500 AN: 5158

South Asian (SAS) AF: 0.0687 AC: 331 AN: 4818

European-Finnish (FIN) AF: 0.0168 AC: 178 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0536 AC: 3643 AN: 67962

Other (OTH) AF: 0.0617 AC: 130 AN: 2108

Alfa AF: 0.0572 Hom.: 497

Bravo AF: 0.0437

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.73
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs8017615; hg19: chr14-54259598;