ENST00000608785.2:n.7C>T

Variant names:

• chr4-184382297-G-A
• rs6831978
• ENST00000608785.2:n.7C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000608785.2(LINC02362):​n.7C>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 ENST00000608785.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02362	NR_125933.1	n.10C>T		non_coding_transcript_exon_variant	Exon 1 of 7
LINC02362	NR_125934.1	n.10C>T		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02362	ENST00000608785.2	n.7C>T		non_coding_transcript_exon_variant	Exon 1 of 7	3
LINC02362	ENST00000610683.5	n.7C>T		non_coding_transcript_exon_variant	Exon 1 of 6	5
LINC02362	ENST00000658007.1	n.7C>T		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.711 AC: 29519 AN: 41490

American (AMR) AF: 0.935 AC: 14312 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2988 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5118 AN: 5186

South Asian (SAS) AF: 0.950 AC: 4585 AN: 4828

European-Finnish (FIN) AF: 0.954 AC: 10116 AN: 10604

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64399 AN: 68026

Other (OTH) AF: 0.896 AC: 1890 AN: 2110

Alfa AF: 0.925 Hom.: 123761

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs6831978; hg19: chr4-185303451;