20-55551451-G-T

Variant names:

• chr20-55551451-G-T
• rs11696973
• ENST00000654685.1:n.918-9378G>T

Variant summary

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

The ENST00000654685.1(LINC01440):​n.918-9378G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,162 control chromosomes in the GnomAD database, including 1,305 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 0.13 (1305 hom., cov: 32)
• Consequence: LINC01440 ENST00000654685.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654685.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01440	ENST00000654685.1		n.918-9378G>T		intron	N/A
	LINC01440	ENST00000664886.1		n.648+83237G>T		intron	N/A
	LINC01440	ENST00000667361.1		n.1480+83237G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19427 AN: 152044 Hom.: 1304 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.128 AC: 19444 AN: 152162 Hom.: 1305 Cov.: 32 AF XY: 0.124 AC XY: 9206 AN XY: 74416

African (AFR) AF: 0.130 AC: 5411 AN: 41500

American (AMR) AF: 0.101 AC: 1541 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3466

East Asian (EAS) AF: 0.0944 AC: 489 AN: 5182

South Asian (SAS) AF: 0.115 AC: 556 AN: 4818

European-Finnish (FIN) AF: 0.0686 AC: 726 AN: 10586

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9782 AN: 68000

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.131 Hom.: 377

Bravo AF: 0.129

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.60
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs11696973; hg19: chr20-54126509;