14-53697318-G-T

Variant names:

• chr14-53697318-G-T
• rs210361
• ENST00000418927.2:n.843-10710C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184212.1(LINC02331):​n.768-10710C>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 NR_184212.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

LINC02331 (HGNC:53251): (long intergenic non-protein coding RNA 2331)

ENSG00000237356 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02331	NR_184212.1	n.768-10710C>A		intron_variant	Intron 6 of 6
LINC02331	NR_184214.1	n.779-10710C>A		intron_variant	Intron 5 of 5
LINC02331	NR_184218.1	n.694-10710C>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.2	n.843-10710C>A		intron_variant	Intron 5 of 5	5
ENSG00000237356	ENST00000648066.1	n.510+9944G>T		intron_variant	Intron 5 of 9
ENSG00000237356	ENST00000663444.1	n.735+9944G>T		intron_variant	Intron 4 of 4

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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.712

Alfa AF: 0.726 Hom.: 54287

Bravo AF: 0.726

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210361; hg19: chr14-54164036;