chr5-3435027-T-C

Position:

• chr5-3435027-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01019 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01019	NR_033898.1	n.460-12405A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01019	ENST00000505443.1	n.460-12405A>G		intron_variant		1
LINC01019	ENST00000662836.1	n.44-12405A>G		intron_variant

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

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.724

Alfa AF: 0.749 Hom.: 71622

Bravo AF: 0.712

Asia WGS AF: 0.816 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs251444; hg19: chr5-3435141;