chr14-53703022-G-A

Position:

• chr14-53703022-G-A

Variant summary

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

The NR_184221.1(LINC02331):​n.606-16414C>T 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 0.114 in 152,170 control chromosomes in the GnomAD database, including 1,251 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 0.11 (1251 hom., cov: 32)
• Consequence: LINC02331 NR_184221.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02331	NR_184221.1	n.606-16414C>T		intron_variant, non_coding_transcript_variant
LOC105370504	XR_943876.3	n.29876+15648G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02331	ENST00000418927.2	n.843-16414C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000648066.1	n.510+15648G>A		intron_variant, non_coding_transcript_variant
	ENST00000663444.1	n.735+15648G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17336 AN: 152052 Hom.: 1245 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.114 AC: 17376 AN: 152170 Hom.: 1251 Cov.: 32 AF XY: 0.115 AC XY: 8568 AN XY: 74390

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0380

Gnomad4 NFE AF: 0.0752

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0723 Hom.: 246

Bravo AF: 0.122

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210357; hg19: chr14-54169740;