18-70385716-T-C

Variant names:

• chr18-70385716-T-C
• rs1030982
• ENST00000783305.1:n.319-13172T>C

Variant summary

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

The ENST00000783305.1(LINC01909):​n.319-13172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,310 control chromosomes in the GnomAD database, including 19,993 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 0.50 (19993 hom., cov: 28)
• Consequence: LINC01909 ENST00000783305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 3 publications found

Genes affected

LINC01909 (HGNC:52728): (long intergenic non-protein coding RNA 1909)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01909	ENST00000783305.1	n.319-13172T>C		intron_variant	Intron 3 of 3
LINC01909	ENST00000783306.1	n.50-5346T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75752 AN: 151192 Hom.: 19979 Cov.: 28

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.501 AC: 75795 AN: 151310 Hom.: 19993 Cov.: 28 AF XY: 0.507 AC XY: 37412 AN XY: 73862

African (AFR) AF: 0.324 AC: 13342 AN: 41196

American (AMR) AF: 0.559 AC: 8500 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2146 AN: 3460

East Asian (EAS) AF: 0.620 AC: 3162 AN: 5098

South Asian (SAS) AF: 0.654 AC: 3124 AN: 4774

European-Finnish (FIN) AF: 0.566 AC: 5895 AN: 10412

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37930 AN: 67858

Other (OTH) AF: 0.502 AC: 1052 AN: 2096

Alfa AF: 0.542 Hom.: 71677

Bravo AF: 0.492

Asia WGS AF: 0.635 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.69
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1030982; hg19: chr18-68052952;