rs1458991

Positions:

• chr14-53702952-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_184213.1(LINC02331):​n.970T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00996 in 152,276 control chromosomes in the GnomAD database, including 14 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 0.010 (14 hom., cov: 32)
• Consequence: LINC02331 NR_184213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

LINC02331 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02331	NR_184213.1	n.970T>C		non_coding_transcript_exon_variant	7/7
LINC02331	NR_184212.1	n.768-16344T>C		intron_variant
LINC02331	NR_184214.1	n.779-16344T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02331	ENST00000418927.2	n.843-16344T>C		intron_variant		5
ENSG00000237356	ENST00000648066.1	n.510+15578A>G		intron_variant
ENSG00000237356	ENST00000663444.1	n.735+15578A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00997 AC: 1517 AN: 152158 Hom.: 14 Cov.: 32

Gnomad AFR AF: 0.00263

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.00765

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

GnomAD4 genome AF: 0.00996 AC: 1517 AN: 152276 Hom.: 14 Cov.: 32 AF XY: 0.0101 AC XY: 749 AN XY: 74446

Gnomad4 AFR AF: 0.00262

Gnomad4 AMR AF: 0.0107

Gnomad4 ASJ AF: 0.00403

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.0157

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.00757

Alfa AF: 0.0111 Hom.: 1

Bravo AF: 0.00854

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	12
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458991; hg19: chr14-54169670;