18-71772119-T-C

Variant names:

• chr18-71772119-T-C
• rs17085111
• ENST00000583756.2:n.244+10071A>G

Variant summary

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

The ENST00000583756.2(LINC01899):​n.244+10071A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,934 control chromosomes in the GnomAD database, including 12,577 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 0.40 (12577 hom., cov: 32)
• Consequence: LINC01899 ENST00000583756.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.559 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+10071A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01899	ENST00000583756.2	TSL:3	n.244+10071A>G		intron	N/A
	LINC01899	ENST00000764766.1		n.168+10071A>G		intron	N/A
	LINC01899	ENST00000764767.1		n.240+10071A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60303 AN: 151816 Hom.: 12570 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.397 AC: 60335 AN: 151934 Hom.: 12577 Cov.: 32 AF XY: 0.392 AC XY: 29135 AN XY: 74258

African (AFR) AF: 0.464 AC: 19225 AN: 41432

American (AMR) AF: 0.394 AC: 6010 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3466

East Asian (EAS) AF: 0.577 AC: 2967 AN: 5144

South Asian (SAS) AF: 0.420 AC: 2020 AN: 4814

European-Finnish (FIN) AF: 0.211 AC: 2235 AN: 10576

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24934 AN: 67938

Other (OTH) AF: 0.399 AC: 837 AN: 2098

Alfa AF: 0.377 Hom.: 4777

Bravo AF: 0.413

Asia WGS AF: 0.475 AC: 1652 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	4.6
DANN	Benign	0.56
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17085111; hg19: chr18-69439355;