rs10170218

Positions:

• chr2-187949717-A-C

Variant summary

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

The ENST00000434418.2(LINC01090):​n.496+85879T>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 0.254 in 152,058 control chromosomes in the GnomAD database, including 5,116 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 0.25 (5116 hom., cov: 32)
• Consequence: LINC01090 ENST00000434418.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01090	ENST00000434418.2	n.496+85879T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38549 AN: 151940 Hom.: 5108 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.254 AC: 38574 AN: 152058 Hom.: 5116 Cov.: 32 AF XY: 0.254 AC XY: 18915 AN XY: 74334

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.258

Alfa AF: 0.269 Hom.: 11353

Bravo AF: 0.249

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10170218; hg19: chr2-188814444;