20-55329874-A-T

Variant names:

• chr20-55329874-A-T
• rs6069250
• ENST00000827372.1:n.409+2271A>T

Variant summary

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

The ENST00000827372.1(LINC01440):​n.409+2271A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,042 control chromosomes in the GnomAD database, including 44,549 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 0.71 (44549 hom., cov: 31)
• Consequence: LINC01440 ENST00000827372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827372.1. 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
	LINC01440	ENST00000827372.1		n.409+2271A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108515 AN: 151924 Hom.: 44539 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.714 AC: 108535 AN: 152042 Hom.: 44549 Cov.: 31 AF XY: 0.725 AC XY: 53910 AN XY: 74318

African (AFR) AF: 0.271 AC: 11245 AN: 41448

American (AMR) AF: 0.844 AC: 12858 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2715 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5173 AN: 5178

South Asian (SAS) AF: 0.879 AC: 4234 AN: 4816

European-Finnish (FIN) AF: 0.943 AC: 9985 AN: 10592

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59806 AN: 67984

Other (OTH) AF: 0.743 AC: 1569 AN: 2112

Alfa AF: 0.786 Hom.: 6072

Bravo AF: 0.685

Asia WGS AF: 0.900 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.58
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6069250;

hg19: chr20-53946413;

COSMIC: COSV60105258;