rs212559

Variant names:

• chr20-55453267-G-A
• rs212559
• ENST00000416190.5:n.1092+834G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000416190.5(LINC01440):​n.1092+834G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 152,114 control chromosomes in the GnomAD database, including 44 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 0.014 (44 hom., cov: 32)
• Consequence: LINC01440 ENST00000416190.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• 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=-0.84).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0145 (2204/152114) while in subpopulation AFR AF = 0.047 (1949/41512). AF 95% confidence interval is 0.0452. There are 44 homozygotes in GnomAd4. There are 1071 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 44 gene

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	ENST00000416190.5	n.1092+834G>A		intron_variant	Intron 6 of 7	5
LINC01440	ENST00000627300.2	n.189-13550G>A		intron_variant	Intron 1 of 3	5
LINC01440	ENST00000654685.1	n.669+4298G>A		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.0144 AC: 2192 AN: 151996 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00917

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000809

Gnomad OTH AF: 0.0115

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

GnomAD4 genome AF: 0.0145 AC: 2204 AN: 152114 Hom.: 44 Cov.: 32 AF XY: 0.0144 AC XY: 1071 AN XY: 74368

African (AFR) AF: 0.0470 AC: 1949 AN: 41512

American (AMR) AF: 0.00916 AC: 140 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 33 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10572

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000809 AC: 55 AN: 67968

Other (OTH) AF: 0.0114 AC: 24 AN: 2112

Alfa AF: 0.0105 Hom.: 1

Bravo AF: 0.0163

Asia WGS AF: 0.00493 AC: 17 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.70
DANN	Benign	0.70
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs212559; hg19: chr20-54069805;