chr14-53697318-G-T

Variant names:

• chr14-53697318-G-T
• rs210361
• ENST00000418927.3:n.843-10710C>A

Variant summary

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

The ENST00000418927.3(LINC02331):​n.843-10710C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,148 control chromosomes in the GnomAD database, including 40,913 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 0.73 (40913 hom., cov: 32)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418927.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02331	NR_184212.1		n.768-10710C>A		intron	N/A
	LINC02331	NR_184214.1		n.779-10710C>A		intron	N/A
	LINC02331	NR_184218.1		n.694-10710C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02331	ENST00000418927.3	TSL:5	n.843-10710C>A		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.850+9944G>T		intron	N/A
	DDHD1-DT	ENST00000663444.2		n.792+9944G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111225 AN: 152030 Hom.: 40912 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.731 AC: 111273 AN: 152148 Hom.: 40913 Cov.: 32 AF XY: 0.739 AC XY: 54986 AN XY: 74384

African (AFR) AF: 0.675 AC: 28019 AN: 41486

American (AMR) AF: 0.769 AC: 11772 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3468

East Asian (EAS) AF: 0.913 AC: 4724 AN: 5176

South Asian (SAS) AF: 0.772 AC: 3715 AN: 4812

European-Finnish (FIN) AF: 0.802 AC: 8498 AN: 10594

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49647 AN: 67994

Other (OTH) AF: 0.712 AC: 1503 AN: 2112

Alfa AF: 0.727 Hom.: 75161

Bravo AF: 0.726

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.54
DANN	Benign	0.26
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs210361; hg19: chr14-54164036;