rs17085106

Variant names:

• chr18-71771837-G-T
• rs17085106
• ENST00000583756.2:n.244+10353C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000583756.2(LINC01899):​n.244+10353C>A variant causes a intron 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 ENST00000583756.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583756.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01899	NR_126324.1		n.37+10353C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01899	ENST00000583756.2	TSL:3	n.244+10353C>A		intron	N/A
	LINC01899	ENST00000764766.1		n.168+10353C>A		intron	N/A
	LINC01899	ENST00000764767.1		n.240+10353C>A		intron	N/A

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

African (AFR) AF: 0.170 AC: 6934 AN: 40852

American (AMR) AF: 0.0310 AC: 461 AN: 14866

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3466

East Asian (EAS) AF: 0.000402 AC: 2 AN: 4978

South Asian (SAS) AF: 0.0463 AC: 218 AN: 4710

European-Finnish (FIN) AF: 0.0102 AC: 107 AN: 10458

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1123 AN: 67680

Other (OTH) AF: 0.0585 AC: 121 AN: 2068

Alfa AF: 0.0299 Hom.: 772

Bravo AF: 0.0653

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.27
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs17085106; hg19: chr18-69439073;