rs6831978

Positions:

• chr4-184382297-G-A
• chr4-184382297-G-C
• chr4-184382297-G-T

Variant summary

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

The NR_125934.1(LINC02362):​n.10C>T 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 0.881 in 152,232 control chromosomes in the GnomAD database, including 59,924 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 0.88 (59922 hom., cov: 33)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: LINC02362 NR_125934.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

Genes affected

LINC02362 (HGNC:53284): (long intergenic non-protein coding RNA 2362)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02362	NR_125934.1	n.10C>T		non_coding_transcript_exon_variant	1/6
LINC02362	NR_125933.1	n.10C>T		non_coding_transcript_exon_variant	1/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02362	ENST00000667133.1	n.120C>T		non_coding_transcript_exon_variant	1/7

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133958 AN: 152108 Hom.: 59889 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.900

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.881 AC: 134045 AN: 152226 Hom.: 59922 Cov.: 33 AF XY: 0.882 AC XY: 65690 AN XY: 74438

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.896

Alfa AF: 0.931 Hom.: 90826

Bravo AF: 0.872

Asia WGS AF: 0.927 AC: 3224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6831978; hg19: chr4-185303451;