rs10181512

Positions:

• chr2-187931567-T-C
• chr2-187931567-T-G

Variant summary

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

The ENST00000434418.2(LINC01090):​n.496+104029A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,884 control chromosomes in the GnomAD database, including 25,768 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 0.58 (25768 hom., cov: 31)
• Consequence: LINC01090 ENST00000434418.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01090	ENST00000434418.2	n.496+104029A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88065 AN: 151766 Hom.: 25743 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.580 AC: 88137 AN: 151884 Hom.: 25768 Cov.: 31 AF XY: 0.581 AC XY: 43082 AN XY: 74210

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.550

Alfa AF: 0.558 Hom.: 41986

Bravo AF: 0.589

Asia WGS AF: 0.706 AC: 2456 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	1.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10181512; hg19: chr2-188796294;