20-55564428-T-G

Variant names:

• chr20-55564428-T-G
• rs6069325
• ENST00000654685.1:n.1000+3517T>G

Variant summary

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

The ENST00000654685.1(LINC01440):​n.1000+3517T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,090 control chromosomes in the GnomAD database, including 1,578 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 0.14 (1578 hom., cov: 30)
• Consequence: LINC01440 ENST00000654685.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 3 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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	ENST00000654685.1	n.1000+3517T>G		intron_variant	Intron 7 of 7
LINC01440	ENST00000664886.1	n.648+96214T>G		intron_variant	Intron 4 of 5
LINC01440	ENST00000667361.1	n.1480+96214T>G		intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21287 AN: 150976 Hom.: 1575 Cov.: 30

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.141 AC: 21307 AN: 151090 Hom.: 1578 Cov.: 30 AF XY: 0.137 AC XY: 10104 AN XY: 73800

African (AFR) AF: 0.133 AC: 5461 AN: 41146

American (AMR) AF: 0.114 AC: 1715 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3468

East Asian (EAS) AF: 0.0945 AC: 485 AN: 5134

South Asian (SAS) AF: 0.123 AC: 588 AN: 4788

European-Finnish (FIN) AF: 0.0943 AC: 978 AN: 10376

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10918 AN: 67772

Other (OTH) AF: 0.136 AC: 285 AN: 2096

Alfa AF: 0.155 Hom.: 221

Bravo AF: 0.141

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.65
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6069325; hg19: chr20-54139486;