5-3428851-T-C

Variant names:

• chr5-3428851-T-C
• rs42742
• ENST00000505443.1:n.460-6229A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505443.1(LINC01019):​n.460-6229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,156 control chromosomes in the GnomAD database, including 3,682 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 0.22 (3682 hom., cov: 33)
• Consequence: LINC01019 ENST00000505443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01019	NR_033898.1	n.460-6229A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01019	ENST00000505443.1	n.460-6229A>G		intron_variant	Intron 2 of 4	1
LINC01019	ENST00000662836.1	n.44-6229A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33062 AN: 152038 Hom.: 3676 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.217 AC: 33089 AN: 152156 Hom.: 3682 Cov.: 33 AF XY: 0.219 AC XY: 16284 AN XY: 74384

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.242

Alfa AF: 0.175 Hom.: 583

Bravo AF: 0.212

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs42742; hg19: chr5-3428965;