20-10869816-G-T

Variant names:

• chr20-10869816-G-T
• rs1884136
• ENST00000605292.5:n.99-39010G>T

Variant summary

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

The ENST00000605292.5(ENSG00000270792):​n.99-39010G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,148 control chromosomes in the GnomAD database, including 828 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 0.087 (828 hom., cov: 33)
• Consequence: ENSG00000270792 ENST00000605292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 10 publications found

Genes affected

ENSG00000270792 (HGNC:):

LINC01752 (HGNC:52540): (long intergenic non-protein coding RNA 1752)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605292.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000270792	ENST00000605292.5	TSL:3	n.99-39010G>T		intron	N/A
	LINC01752	ENST00000667822.1		n.332-39010G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13159 AN: 152030 Hom.: 827 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0911

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

GnomAD4 genome AF: 0.0865 AC: 13167 AN: 152148 Hom.: 828 Cov.: 33 AF XY: 0.0890 AC XY: 6621 AN XY: 74384

African (AFR) AF: 0.0293 AC: 1216 AN: 41522

American (AMR) AF: 0.0657 AC: 1004 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 339 AN: 3464

East Asian (EAS) AF: 0.301 AC: 1547 AN: 5146

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4822

European-Finnish (FIN) AF: 0.0719 AC: 761 AN: 10588

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6943 AN: 68004

Other (OTH) AF: 0.0920 AC: 194 AN: 2108

Alfa AF: 0.102 Hom.: 4022

Bravo AF: 0.0816

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.80
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1884136; hg19: chr20-10850464;