rs4810113

Variant names:

• chr20-58002043-G-A
• rs4810113
• ENST00000836927.1:n.125+481G>A

Variant summary

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

The ENST00000836927.1(LINC01742):​n.125+481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,248 control chromosomes in the GnomAD database, including 1,388 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 0.12 (1388 hom., cov: 32)
• Consequence: LINC01742 ENST00000836927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 1 publications found

Genes affected

LINC01742 (HGNC:52530): (long intergenic non-protein coding RNA 1742)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 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
LINC01742	ENST00000836927.1	n.125+481G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18007 AN: 152128 Hom.: 1385 Cov.: 32

Gnomad AFR AF: 0.0271

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.118 AC: 18019 AN: 152248 Hom.: 1388 Cov.: 32 AF XY: 0.124 AC XY: 9224 AN XY: 74446

African (AFR) AF: 0.0271 AC: 1125 AN: 41566

American (AMR) AF: 0.202 AC: 3095 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3472

East Asian (EAS) AF: 0.158 AC: 816 AN: 5172

South Asian (SAS) AF: 0.193 AC: 931 AN: 4824

European-Finnish (FIN) AF: 0.186 AC: 1978 AN: 10606

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9034 AN: 67996

Other (OTH) AF: 0.122 AC: 258 AN: 2116

Alfa AF: 0.135 Hom.: 2006

Bravo AF: 0.114

Asia WGS AF: 0.147 AC: 509 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	0.0010
DANN	Benign	0.27
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4810113; hg19: chr20-56577099;