rs210359

chr14-53700754-A-C

Variant summary

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

The NR_184221.1(LINC02331):n.606-14146T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 152,286 control chromosomes in the GnomAD database, including 67,800 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 0.94 (67800 hom., cov: 31)
• Consequence: LINC02331 NR_184221.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02331	NR_184221.1	n.606-14146T>G		intron_variant, non_coding_transcript_variant
LOC105370504	XR_943876.3	n.29876+13380A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02331	ENST00000418927.2	n.843-14146T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000648066.1	n.510+13380A>C		intron_variant, non_coding_transcript_variant
	ENST00000663444.1	n.735+13380A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143458 AN: 152168 Hom.: 67747 Cov.: 31

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.949

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.943 AC: 143569 AN: 152286 Hom.: 67800 Cov.: 31 AF XY: 0.941 AC XY: 70074 AN XY: 74458

Gnomad4 AFR AF: 0.986

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.926

Alfa AF: 0.929 Hom.: 130277

Bravo AF: 0.941

Asia WGS AF: 0.871 AC: 3031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.66
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210359; hg19: chr14-54167472;