rs448013

Variant names:

• chr20-55682857-G-A
• rs448013
• ENST00000661549.2:n.127-15231C>T

Variant summary

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

The ENST00000661549.2(ENSG00000287478):​n.127-15231C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 152,104 control chromosomes in the GnomAD database, including 503 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 0.057 (503 hom., cov: 32)
• Consequence: ENSG00000287478 ENST00000661549.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.51
• Publications: 4 publications found

Genes affected

ENSG00000287478 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661549.2. 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
	ENSG00000287478	ENST00000661549.2		n.127-15231C>T		intron	N/A
	LINC01440	ENST00000664886.1		n.832-1766G>A		intron	N/A
	LINC01440	ENST00000667361.1		n.1634-1766G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8725 AN: 151986 Hom.: 505 Cov.: 32

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0574 AC: 8729 AN: 152104 Hom.: 503 Cov.: 32 AF XY: 0.0603 AC XY: 4483 AN XY: 74356

African (AFR) AF: 0.0897 AC: 3722 AN: 41476

American (AMR) AF: 0.0628 AC: 959 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1628 AN: 5176

South Asian (SAS) AF: 0.0713 AC: 343 AN: 4808

European-Finnish (FIN) AF: 0.0339 AC: 359 AN: 10578

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0212 AC: 1439 AN: 67998

Other (OTH) AF: 0.0602 AC: 127 AN: 2110

Alfa AF: 0.0355 Hom.: 123

Bravo AF: 0.0635

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.031
DANN	Benign	0.57
PhyloP100		-3.5

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: rs448013;

hg19: chr20-54257915;

COSMIC: COSV62508882;