20-55345927-A-G

Variant names:

• chr20-55345927-A-G
• rs211902
• ENST00000827372.1:n.526+7019A>G

Variant summary

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

The ENST00000827372.1(LINC01440):​n.526+7019A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,206 control chromosomes in the GnomAD database, including 58,145 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 0.87 (58145 hom., cov: 32)
• Consequence: LINC01440 ENST00000827372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 2 publications found

Genes affected

LINC01440 (HGNC:50762): (long intergenic non-protein coding RNA 1440)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
LINC01440	ENST00000827372.1	n.526+7019A>G		intron_variant	Intron 4 of 4
LINC01440	ENST00000827373.1	n.117+7019A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132584 AN: 152088 Hom.: 58107 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.872 AC: 132675 AN: 152206 Hom.: 58145 Cov.: 32 AF XY: 0.878 AC XY: 65368 AN XY: 74420

African (AFR) AF: 0.780 AC: 32350 AN: 41494

American (AMR) AF: 0.917 AC: 14030 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2871 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5154 AN: 5158

South Asian (SAS) AF: 0.883 AC: 4255 AN: 4820

European-Finnish (FIN) AF: 0.950 AC: 10095 AN: 10622

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61066 AN: 68022

Other (OTH) AF: 0.875 AC: 1847 AN: 2112

Alfa AF: 0.886 Hom.: 7729

Bravo AF: 0.865

Asia WGS AF: 0.944 AC: 3284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs211902; hg19: chr20-53962466;