rs2242226

chr4-188551019-T-C

Variant summary

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

The NR_033869.1(LINC01060):n.343-50749T>C variant causes a intron, non coding transcript 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 NR_033869.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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=-0.89).
• 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/exons	MANE	UniProt
LINC01060	NR_033869.1	n.343-50749T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01060	ENST00000664177.1	n.330+65154T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0257

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.104

Alfa AF: 0.134 Hom.: 682

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2242226; hg19: chr4-189472173;