ENST00000503580.1:n.88-36705C>T

Variant names:

• chr4-188644016-C-T
• rs6834498
• ENST00000503580.1:n.88-36705C>T

Variant summary

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

The ENST00000503580.1(LINC01060):​n.88-36705C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,068 control chromosomes in the GnomAD database, including 2,793 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 (2793 hom., cov: 32)
• Consequence: LINC01060 ENST00000503580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000503580.1	n.88-36705C>T		intron_variant	Intron 1 of 1	3
LINC01060	ENST00000664177.1	n.331-36267C>T		intron_variant	Intron 3 of 3
LINC01060	ENST00000692519.1	n.362-36267C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28637 AN: 151950 Hom.: 2777 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.189 AC: 28703 AN: 152068 Hom.: 2793 Cov.: 32 AF XY: 0.184 AC XY: 13715 AN XY: 74338

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.198

Alfa AF: 0.172 Hom.: 2470

Bravo AF: 0.188

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6834498; hg19: chr4-189565170;