rs17151283

Variant names:

• chr5-124174506-C-T
• rs17151283
• ENST00000628324.2:n.403-111996G>A

Variant summary

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

The ENST00000628324.2(LINC01170):​n.403-111996G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,082 control chromosomes in the GnomAD database, including 1,408 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 (1408 hom., cov: 32)
• Consequence: LINC01170 ENST00000628324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01170	NR_125774.1	n.490-111996G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01170	ENST00000628324.2	n.403-111996G>A		intron_variant	Intron 2 of 3	2
LINC01170	ENST00000653233.2	n.500-37186G>A		intron_variant	Intron 3 of 6
LINC01170	ENST00000657766.2	n.394-37186G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18441 AN: 151964 Hom.: 1408 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.121 AC: 18451 AN: 152082 Hom.: 1408 Cov.: 32 AF XY: 0.118 AC XY: 8784 AN XY: 74338

African (AFR) AF: 0.207 AC: 8596 AN: 41486

American (AMR) AF: 0.0730 AC: 1112 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3472

East Asian (EAS) AF: 0.000968 AC: 5 AN: 5166

South Asian (SAS) AF: 0.0491 AC: 237 AN: 4822

European-Finnish (FIN) AF: 0.108 AC: 1149 AN: 10598

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0991 AC: 6736 AN: 67982

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.100 Hom.: 1449

Bravo AF: 0.121

Asia WGS AF: 0.0330 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.22
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs17151283; hg19: chr5-123510199;