rs867604

Variant names:

• chr14-53786405-G-C
• rs867604
• ENST00000418927.3:n.580+6849C>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+6849C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,190 control chromosomes in the GnomAD database, including 62,886 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 0.90 (62886 hom., cov: 31)
• Consequence: LINC02331 NR_184212.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 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+6849C>G		intron	N/A
	LINC02331	NR_184213.1		n.505+6849C>G		intron	N/A
	LINC02331	NR_184214.1		n.524+6849C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02331	ENST00000418927.3	TSL:5	n.580+6849C>G		intron	N/A
	DDHD1-DT	ENST00000649040.1		n.65+20686G>C		intron	N/A
	DDHD1-DT	ENST00000728781.1		n.177-88099G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136215 AN: 152072 Hom.: 62877 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.895 AC: 136265 AN: 152190 Hom.: 62886 Cov.: 31 AF XY: 0.898 AC XY: 66851 AN XY: 74408

African (AFR) AF: 0.638 AC: 26436 AN: 41456

American (AMR) AF: 0.960 AC: 14668 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3467 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5178

South Asian (SAS) AF: 0.995 AC: 4801 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10624 AN: 10624

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67925 AN: 68028

Other (OTH) AF: 0.931 AC: 1971 AN: 2116

Alfa AF: 0.936 Hom.: 8456

Bravo AF: 0.881

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs867604; hg19: chr14-54253123;