14-53761799-T-C

Variant summary

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

The NR_184221.1(LINC02331):n.506+7002A>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 0.887 in 152,062 control chromosomes in the GnomAD database, including 59,850 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 0.89 (59850 hom., cov: 32)
• Consequence: LINC02331 NR_184221.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02331	NR_184221.1	n.506+7002A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02331	ENST00000418927.2	n.743+7002A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000648066.1	n.611-3859T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134702 AN: 151944 Hom.: 59787 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.887 AC: 134824 AN: 152062 Hom.: 59850 Cov.: 32 AF XY: 0.887 AC XY: 65883 AN XY: 74318

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.904

Alfa AF: 0.878 Hom.: 84988

Bravo AF: 0.895

Asia WGS AF: 0.963 AC: 3348 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.33
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1958654; hg19: chr14-54228517;