5-3435027-T-C

Variant names:

• chr5-3435027-T-C
• rs251444
• ENST00000505443.1:n.460-12405A>G

Variant summary

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

The ENST00000505443.1(LINC01019):​n.460-12405A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,102 control chromosomes in the GnomAD database, including 39,537 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 0.72 (39537 hom., cov: 32)
• Consequence: LINC01019 ENST00000505443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 3 publications found

Genes affected

LINC01019 (HGNC:27742): (long intergenic non-protein coding RNA 1019)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505443.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01019	NR_033898.1		n.460-12405A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01019	ENST00000505443.1	TSL:1	n.460-12405A>G		intron	N/A
	LINC01019	ENST00000662836.1		n.44-12405A>G		intron	N/A
	LINC01019	ENST00000715743.1		n.102-12405A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109051 AN: 151984 Hom.: 39496 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.718 AC: 109160 AN: 152102 Hom.: 39537 Cov.: 32 AF XY: 0.718 AC XY: 53381 AN XY: 74340

African (AFR) AF: 0.631 AC: 26156 AN: 41446

American (AMR) AF: 0.718 AC: 10978 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3468

East Asian (EAS) AF: 0.875 AC: 4528 AN: 5172

South Asian (SAS) AF: 0.798 AC: 3846 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7518 AN: 10582

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51409 AN: 67998

Other (OTH) AF: 0.724 AC: 1527 AN: 2110

Alfa AF: 0.743 Hom.: 159789

Bravo AF: 0.712

Asia WGS AF: 0.816 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs251444; hg19: chr5-3435141;