5-124415394-C-T

Variant names:

• chr5-124415394-C-T
• rs33888
• ENST00000519703.3:n.202-10309G>A

Variant summary

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

The ENST00000519703.3(LINC01170):​n.202-10309G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,006 control chromosomes in the GnomAD database, including 6,998 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 0.27 (6998 hom., cov: 33)
• Consequence: LINC01170 ENST00000519703.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01170	NR_125774.1	n.444+20764G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01170	ENST00000519703.3	n.202-10309G>A		intron_variant	Intron 1 of 5	5
LINC01170	ENST00000653233.2	n.241+22995G>A		intron_variant	Intron 1 of 6
LINC01170	ENST00000657766.2	n.232+23001G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41021 AN: 151888 Hom.: 6973 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.270 AC: 41061 AN: 152006 Hom.: 6998 Cov.: 33 AF XY: 0.278 AC XY: 20649 AN XY: 74292

African (AFR) AF: 0.120 AC: 4991 AN: 41458

American (AMR) AF: 0.418 AC: 6390 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3464

East Asian (EAS) AF: 0.751 AC: 3885 AN: 5170

South Asian (SAS) AF: 0.384 AC: 1842 AN: 4796

European-Finnish (FIN) AF: 0.262 AC: 2775 AN: 10582

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18843 AN: 67936

Other (OTH) AF: 0.302 AC: 636 AN: 2108

Alfa AF: 0.257 Hom.: 748

Bravo AF: 0.280

Asia WGS AF: 0.538 AC: 1868 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.70
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs33888; hg19: chr5-123751087;