17-69961633-G-C

Position:

• chr17-69961633-G-C

Variant summary

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

The ENST00000455460.6(LINC01497):​n.66G>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 ENST00000455460.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

Genes affected

LINC01497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.69961633G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01497	ENST00000455460.6	n.66G>C		non_coding_transcript_exon_variant	1/5	3
LINC01497	ENST00000692412.1	n.13G>C		non_coding_transcript_exon_variant	1/4
LINC01497	ENST00000702106.1	n.13G>C		non_coding_transcript_exon_variant	1/5

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.857

Gnomad4 OTH exome AF: 0.875

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

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.742

Alfa AF: 0.579 Hom.: 1414

Bravo AF: 0.791

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180067; hg19: chr17-67957774;