chr18-1287909-A-T

Variant names:

• chr18-1287909-A-T
• rs1120867
• ENST00000577403.6:n.204-9276T>A

Variant summary

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

The ENST00000577403.6(LINC00470):​n.204-9276T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 151,828 control chromosomes in the GnomAD database, including 33,635 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 0.66 (33635 hom., cov: 31)
• Consequence: LINC00470 ENST00000577403.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 1 publications found

Genes affected

LINC00470 (HGNC:1225): (long intergenic non-protein coding RNA 470)

ENSG00000263551 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00470	NR_023925.1	n.335-11832T>A		intron_variant	Intron 3 of 6
LINC00470	NR_023926.1	n.279-11822T>A		intron_variant	Intron 2 of 5
LINC00470	NR_023927.1	n.279-15398T>A		intron_variant	Intron 2 of 3
LINC00470	NR_110327.1	n.279-11832T>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00470	ENST00000577403.6	n.204-9276T>A		intron_variant	Intron 4 of 7	1
LINC00470	ENST00000577867.5	n.300-15398T>A		intron_variant	Intron 2 of 3	1
LINC00470	ENST00000581212.1	n.335-11832T>A		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100557 AN: 151710 Hom.: 33592 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.663 AC: 100656 AN: 151828 Hom.: 33635 Cov.: 31 AF XY: 0.663 AC XY: 49203 AN XY: 74178

African (AFR) AF: 0.745 AC: 30862 AN: 41448

American (AMR) AF: 0.622 AC: 9468 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2298 AN: 3466

East Asian (EAS) AF: 0.642 AC: 3309 AN: 5158

South Asian (SAS) AF: 0.594 AC: 2864 AN: 4820

European-Finnish (FIN) AF: 0.672 AC: 7060 AN: 10510

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42505 AN: 67872

Other (OTH) AF: 0.658 AC: 1391 AN: 2114

Alfa AF: 0.648 Hom.: 3980

Bravo AF: 0.664

Asia WGS AF: 0.626 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.031
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1120867; hg19: chr18-1287910;