4-188665925-C-T

Variant names:

• chr4-188665925-C-T
• rs7659062
• ENST00000503580.1:n.88-14796C>T

Variant summary

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

The ENST00000503580.1(LINC01060):​n.88-14796C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,948 control chromosomes in the GnomAD database, including 2,068 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 0.16 (2068 hom., cov: 32)
• Consequence: LINC01060 ENST00000503580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 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.88-14796C>T		intron_variant	Intron 1 of 1	3
LINC01060	ENST00000664177.1	n.331-14358C>T		intron_variant	Intron 3 of 3
LINC01060	ENST00000692519.1	n.362-14358C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24654 AN: 151830 Hom.: 2065 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.162 AC: 24678 AN: 151948 Hom.: 2068 Cov.: 32 AF XY: 0.157 AC XY: 11683 AN XY: 74278

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0828

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.170

Alfa AF: 0.158 Hom.: 4242

Bravo AF: 0.162

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7659062; hg19: chr4-189587079;