rs17085106

chr18-71771837-G-T

Variant summary

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

The NR_126324.1(LINC01899):n.37+10353C>A 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 0.0603 in 150,276 control chromosomes in the GnomAD database, including 612 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 0.060 (612 hom., cov: 33)
• Consequence: LINC01899 NR_126324.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

LINC01899 (HGNC:52718): (long intergenic non-protein coding RNA 1899)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01899	NR_126324.1	n.37+10353C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01899	ENST00000583756.1	n.37+10353C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0602 AC: 9036 AN: 150156 Hom.: 612 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00442

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.000401

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.0596

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

GnomAD4 genome AF: 0.0603 AC: 9062 AN: 150276 Hom.: 612 Cov.: 33 AF XY: 0.0586 AC XY: 4294 AN XY: 73294

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.000402

Gnomad4 SAS AF: 0.0463

Gnomad4 FIN AF: 0.0102

Gnomad4 NFE AF: 0.0166

Gnomad4 OTH AF: 0.0585

Alfa AF: 0.0240 Hom.: 228

Bravo AF: 0.0653

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
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: rs17085106; hg19: chr18-69439073;