ENST00000640190.1:n.2531+798T>C

Variant names:

• chr9-27261032-A-G
• rs1853186
• ENST00000640190.1:n.2531+798T>C

Variant summary

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

The ENST00000640190.1(LINC00032):​n.2531+798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,108 control chromosomes in the GnomAD database, including 35,025 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 0.68 (35025 hom., cov: 32)
• Consequence: LINC00032 ENST00000640190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

Genes affected

LINC00032 (HGNC:):

LINC00032 (HGNC:16506): (long intergenic non-protein coding RNA 32)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REXO6P	NR_026679.1	n.2531+798T>C		intron_variant	Intron 13 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00032	ENST00000640190.1	n.2531+798T>C		intron_variant	Intron 13 of 16	1
LINC00032	ENST00000638495.1	n.525+798T>C		intron_variant	Intron 5 of 9	6

Frequencies

GnomAD3 genomes AF: 0.678 AC: 103003 AN: 151988 Hom.: 35012 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.678 AC: 103061 AN: 152108 Hom.: 35025 Cov.: 32 AF XY: 0.683 AC XY: 50774 AN XY: 74362

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.660

Alfa AF: 0.659 Hom.: 43495

Bravo AF: 0.675

Asia WGS AF: 0.778 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1853186; hg19: chr9-27261030;