chr18-71772119-T-C

Position:

• chr18-71772119-T-C

Variant summary

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

The NR_126324.1(LINC01899):​n.37+10071A>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 0.397 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 NR_126324.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

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 (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01899	NR_126324.1	n.37+10071A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01899	ENST00000583756.1	n.37+10071A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.399

Alfa AF: 0.376 Hom.: 3814

Bravo AF: 0.413

Asia WGS AF: 0.475 AC: 1652 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	4.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17085111; hg19: chr18-69439355;