ENST00000420427.3:n.90G>C

Variant names:

• chr17-69961633-G-C
• rs180067
• ENST00000420427.3:n.90G>C

Variant summary

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

The ENST00000420427.3(LINC01497):​n.90G>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 0.763 in 152,414 control chromosomes in the GnomAD database, including 45,226 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 0.76 (45155 hom., cov: 42)
  • Exomes 𝑓: 0.87 (71 hom.)
• Consequence: LINC01497 ENST00000420427.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 7 publications found

Genes affected

LINC01497 (HGNC:51163): (long intergenic non-protein coding RNA 1497)

ENSG00000295979 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420427.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01497	NR_110874.1		n.-74G>C		upstream_gene	N/A
	LINC01497	NR_110875.1		n.-74G>C		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01497	ENST00000420427.3	TSL:3	n.90G>C		non_coding_transcript_exon	Exon 1 of 5
	LINC01497	ENST00000455460.7	TSL:3	n.90G>C		non_coding_transcript_exon	Exon 1 of 5
	LINC01497	ENST00000654068.2		n.402G>C		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116054 AN: 152112 Hom.: 45092 Cov.: 42

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.739

GnomAD4 exome AF: 0.870 AC: 160 AN: 184 Hom.: 71 AF XY: 0.861 AC XY: 124 AN XY: 144

African (AFR) AF: 1.00 AC: 6 AN: 6

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 1.00 AC: 8 AN: 8

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.857 AC: 120 AN: 140

Other (OTH) AF: 0.875 AC: 14 AN: 16

GnomAD4 genome AF: 0.763 AC: 116176 AN: 152230 Hom.: 45155 Cov.: 42 AF XY: 0.766 AC XY: 57013 AN XY: 74432

African (AFR) AF: 0.936 AC: 38922 AN: 41592

American (AMR) AF: 0.753 AC: 11514 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3472

East Asian (EAS) AF: 0.959 AC: 4977 AN: 5188

South Asian (SAS) AF: 0.843 AC: 4076 AN: 4834

European-Finnish (FIN) AF: 0.670 AC: 7091 AN: 10586

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44644 AN: 67942

Other (OTH) AF: 0.742 AC: 1569 AN: 2114

Alfa AF: 0.579 Hom.: 1414

Bravo AF: 0.791

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.41
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs180067; hg19: chr17-67957774;