rs32732

Variant names:

• chr5-3456649-G-A
• rs32732
• ENST00000505443.1:n.460-34027C>T

Variant summary

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

The ENST00000505443.1(LINC01019):​n.460-34027C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,166 control chromosomes in the GnomAD database, including 52,463 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 0.83 (52463 hom., cov: 32)
• Consequence: LINC01019 ENST00000505443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

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

LINC02162 (HGNC:53023): (long intergenic non-protein coding RNA 2162)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01019	NR_033898.1	n.460-34027C>T		intron_variant	Intron 2 of 4
LINC02162	NR_147000.1	n.230+2862G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01019	ENST00000505443.1	n.460-34027C>T		intron_variant	Intron 2 of 4	1
LINC02162	ENST00000512521.1	n.230+2862G>A		intron_variant	Intron 2 of 2	4
LINC01019	ENST00000662836.1	n.44-34027C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125805 AN: 152048 Hom.: 52435 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.827 AC: 125890 AN: 152166 Hom.: 52463 Cov.: 32 AF XY: 0.829 AC XY: 61652 AN XY: 74392

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.854

Alfa AF: 0.849 Hom.: 9337

Bravo AF: 0.824

Asia WGS AF: 0.824 AC: 2866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs32732; hg19: chr5-3456763;