rs180051

chr17-69981276-T-C

Variant summary

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

The NR_110874.1(LINC01497):n.335T>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 0.19 in 152,018 control chromosomes in the GnomAD database, including 3,189 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 0.19 (3188 hom., cov: 32)
  • Exomes 𝑓: 0.39 (1 hom.)
• Consequence: LINC01497 NR_110874.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01497	NR_110874.1	n.335T>C		non_coding_transcript_exon_variant	3/5
LINC01497	NR_110875.1	n.308T>C		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01497	ENST00000649355.1	n.368T>C		non_coding_transcript_exon_variant	3/8

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28874 AN: 151882 Hom.: 3184 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.0620

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.180

GnomAD4 exome AF: 0.389 AC: 7 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.375 AC XY: 6 AN XY: 16

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.625

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.190 AC: 28905 AN: 152000 Hom.: 3188 Cov.: 32 AF XY: 0.183 AC XY: 13600 AN XY: 74302

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.0626

Gnomad4 FIN AF: 0.0956

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.177

Alfa AF: 0.182 Hom.: 364

Bravo AF: 0.200

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.8
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180051; hg19: chr17-67977417;