rs17126951

Variant names:

• chr14-53810072-C-T
• rs17126951
• ENST00000418927.3:n.438-16676G>A

Variant summary

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

The ENST00000418927.3(LINC02331):​n.438-16676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0839 in 152,036 control chromosomes in the GnomAD database, including 1,529 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 0.084 (1529 hom., cov: 32)
• Consequence: LINC02331 ENST00000418927.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.289-10294G>A		intron_variant	Intron 2 of 6
LINC02331	NR_184213.1	n.289-10294G>A		intron_variant	Intron 2 of 6
LINC02331	NR_184214.1	n.382-16676G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.3	n.438-16676G>A		intron_variant	Intron 2 of 5	5
DDHD1-DT	ENST00000649040.1	n.65+44353C>T		intron_variant	Intron 1 of 2
DDHD1-DT	ENST00000728781.1	n.177-64432C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12693 AN: 151918 Hom.: 1515 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.0207

Gnomad SAS AF: 0.0134

Gnomad FIN AF: 0.00255

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00920

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0839 AC: 12752 AN: 152036 Hom.: 1529 Cov.: 32 AF XY: 0.0817 AC XY: 6071 AN XY: 74326

African (AFR) AF: 0.269 AC: 11145 AN: 41462

American (AMR) AF: 0.0400 AC: 609 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.00808 AC: 28 AN: 3464

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5168

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4830

European-Finnish (FIN) AF: 0.00255 AC: 27 AN: 10600

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00920 AC: 625 AN: 67952

Other (OTH) AF: 0.0644 AC: 136 AN: 2112

Alfa AF: 0.0315 Hom.: 451

Bravo AF: 0.0946

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		-0.031
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17126951; hg19: chr14-54276790;