rs17501712

chr5-124235467-G-T

Variant summary

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

The NR_125774.1(LINC01170):n.489+150762C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,010 control chromosomes in the GnomAD database, including 1,184 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 0.12 (1184 hom., cov: 32)
• Consequence: LINC01170 NR_125774.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

LINC01170 (HGNC:49542): (long intergenic non-protein coding RNA 1170)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01170	NR_125774.1	n.489+150762C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01170	ENST00000628324.2	n.402+150762C>A		intron_variant, non_coding_transcript_variant		2
LINC01170	ENST00000653233.1	n.495+82182C>A		intron_variant, non_coding_transcript_variant
LINC01170	ENST00000657766.1	n.343+70709C>A		intron_variant, non_coding_transcript_variant
LINC01170	ENST00000662643.1	n.343+70709C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17764 AN: 151894 Hom.: 1184 Cov.: 32

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.123

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.117 AC: 17759 AN: 152010 Hom.: 1184 Cov.: 32 AF XY: 0.115 AC XY: 8540 AN XY: 74292

Gnomad4 AFR AF: 0.0706

Gnomad4 AMR AF: 0.0830

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.121

Alfa AF: 0.140 Hom.: 880

Bravo AF: 0.107

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	-0.87
Cadd	Benign	7.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17501712; hg19: chr5-123571160;