rs180067

Positions:

• chr17-69961633-G-A
• chr17-69961633-G-C
• chr17-69961633-G-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2 BP4_Strong BS1

The ENST00000455460.6(LINC01497):​n.66G>A 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 0.0142 in 151,920 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.014 (0 hom., cov: 42)
  • Exomes 𝑓: 0.016 (0 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 Likely_benign. Variant got -6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0142 (2154/151738) while in subpopulation NFE AF= 0.0225 (1525/67638). AF 95% confidence interval is 0.0216. There are 0 homozygotes in gnomad4. There are 1061 alleles in male gnomad4 subpopulation. Median coverage is 42. This position pass quality control queck.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0142 AC: 2154 AN: 151620 Hom.: 0 Cov.: 42

Gnomad AFR AF: 0.00440

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00478

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0225

Gnomad OTH AF: 0.0110

GnomAD4 exome AF: 0.0165 AC: 3 AN: 182 Hom.: 0 AF XY: 0.0141 AC XY: 2 AN XY: 142

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.0145

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0142 AC: 2154 AN: 151738 Hom.: 0 Cov.: 42 AF XY: 0.0143 AC XY: 1061 AN XY: 74170

Gnomad4 AFR AF: 0.00438

Gnomad4 AMR AF: 0.00478

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00414

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0225

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0130 Hom.: 1414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.91

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;