4-188644016-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000664177.2	n.338-36267C>T		intron_variant	Intron 3 of 3
LINC01060	ENST00000692519.2	n.389-36267C>T		intron_variant	Intron 4 of 4
LINC01060	ENST00000806915.1	n.278-36267C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.227 AC: 9421 AN: 41458

American (AMR) AF: 0.167 AC: 2551 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.100 AC: 519 AN: 5166

South Asian (SAS) AF: 0.200 AC: 965 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1502 AN: 10594

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12617 AN: 67974

Other (OTH) AF: 0.198 AC: 417 AN: 2110

Alfa AF: 0.177 Hom.: 3721

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6834498; hg19: chr4-189565170;