18-1306067-C-T

Variant names:

• chr18-1306067-C-T
• rs987611
• ENST00000577403.6:n.204-27434G>A

Variant summary

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

The ENST00000577403.6(LINC00470):​n.204-27434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,662 control chromosomes in the GnomAD database, including 15,388 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 0.44 (15388 hom., cov: 33)
• Consequence: LINC00470 ENST00000577403.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00470	NR_023925.1	n.335-29990G>A		intron_variant	Intron 3 of 6
LINC00470	NR_023926.1	n.279-29980G>A		intron_variant	Intron 2 of 5
LINC00470	NR_023927.1	n.279-33556G>A		intron_variant	Intron 2 of 3
LINC00470	NR_110327.1	n.279-29990G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00470	ENST00000577403.6	n.204-27434G>A		intron_variant	Intron 4 of 7	1
LINC00470	ENST00000577867.5	n.300-33556G>A		intron_variant	Intron 2 of 3	1
LINC00470	ENST00000581212.1	n.335-29990G>A		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67303 AN: 151544 Hom.: 15380 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.444 AC: 67346 AN: 151662 Hom.: 15388 Cov.: 33 AF XY: 0.445 AC XY: 32996 AN XY: 74070

African (AFR) AF: 0.332 AC: 13739 AN: 41384

American (AMR) AF: 0.490 AC: 7477 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1527 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2199 AN: 5146

South Asian (SAS) AF: 0.370 AC: 1780 AN: 4814

European-Finnish (FIN) AF: 0.524 AC: 5483 AN: 10460

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33409 AN: 67834

Other (OTH) AF: 0.465 AC: 980 AN: 2106

Alfa AF: 0.471 Hom.: 27477

Bravo AF: 0.440

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.43
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs987611; hg19: chr18-1306068;