chr5-124415366-T-C

Variant names:

• chr5-124415366-T-C
• rs33889
• ENST00000519703.3:n.202-10281A>G

Variant summary

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

The ENST00000519703.3(LINC01170):​n.202-10281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,276 control chromosomes in the GnomAD database, including 53,075 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 0.83 (53075 hom., cov: 33)
• Consequence: LINC01170 ENST00000519703.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01170	NR_125774.1	n.444+20792A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01170	ENST00000519703.3	n.202-10281A>G		intron_variant	Intron 1 of 5	5
LINC01170	ENST00000653233.2	n.241+23023A>G		intron_variant	Intron 1 of 6
LINC01170	ENST00000657766.2	n.232+23029A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126322 AN: 152158 Hom.: 53022 Cov.: 33

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.830 AC: 126433 AN: 152276 Hom.: 53075 Cov.: 33 AF XY: 0.828 AC XY: 61613 AN XY: 74444

African (AFR) AF: 0.945 AC: 39269 AN: 41572

American (AMR) AF: 0.857 AC: 13112 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2784 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4715 AN: 5182

South Asian (SAS) AF: 0.720 AC: 3471 AN: 4822

European-Finnish (FIN) AF: 0.741 AC: 7855 AN: 10594

Middle Eastern (MID) AF: 0.846 AC: 247 AN: 292

European-Non Finnish (NFE) AF: 0.772 AC: 52527 AN: 68018

Other (OTH) AF: 0.830 AC: 1754 AN: 2112

Alfa AF: 0.805 Hom.: 87968

Bravo AF: 0.848

Asia WGS AF: 0.832 AC: 2891 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.46
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs33889; hg19: chr5-123751059;