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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984001	XR_007067757.1	n.236-15231C>T		intron_variant	Intron 2 of 4
LOC107984001	XR_936884.3	n.236-15231C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287478	ENST00000661549.2	n.127-15231C>T		intron_variant	Intron 1 of 4
LINC01440	ENST00000664886.1	n.832-1766G>A		intron_variant	Intron 5 of 5
LINC01440	ENST00000667361.1	n.1634-1766G>A		intron_variant	Intron 8 of 8

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 v4.3

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

Other links and lift over

dbSNP: rs448013; hg19: chr20-54257915; COSMIC: COSV62508882;