ENST00000503458.9:n.330-50749T>C

Variant names:

• chr4-188551019-T-C
• rs2242226
• ENST00000503458.9:n.330-50749T>C

Variant summary

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

The ENST00000503458.9(LINC01060):​n.330-50749T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,196 control chromosomes in the GnomAD database, including 1,209 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 0.11 (1209 hom., cov: 33)
• Consequence: LINC01060 ENST00000503458.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01060	NR_033869.1	n.343-50749T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000503458.9	n.330-50749T>C		intron_variant	Intron 3 of 3	3
LINC01060	ENST00000503580.1	n.87+65154T>C		intron_variant	Intron 1 of 1	3
LINC01060	ENST00000510005.7	n.387-50749T>C		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16688 AN: 152078 Hom.: 1207 Cov.: 33

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.110 AC: 16682 AN: 152196 Hom.: 1209 Cov.: 33 AF XY: 0.114 AC XY: 8454 AN XY: 74398

African (AFR) AF: 0.0257 AC: 1069 AN: 41548

American (AMR) AF: 0.106 AC: 1626 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3472

East Asian (EAS) AF: 0.120 AC: 619 AN: 5178

South Asian (SAS) AF: 0.143 AC: 688 AN: 4818

European-Finnish (FIN) AF: 0.219 AC: 2312 AN: 10566

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9646 AN: 68012

Other (OTH) AF: 0.104 AC: 221 AN: 2116

Alfa AF: 0.135 Hom.: 778

Bravo AF: 0.0970

Asia WGS AF: 0.146 AC: 506 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.74
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2242226; hg19: chr4-189472173;