rs2174899

Variant names:

• chr18-76579863-T-C
• rs2174899
• ENST00000583578.6:n.326-30982T>C

Variant summary

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

The ENST00000583578.6(LINC00683):​n.326-30982T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,240 control chromosomes in the GnomAD database, including 1,991 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 0.16 (1991 hom., cov: 34)
• Consequence: LINC00683 ENST00000583578.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

LINC00683 (HGNC:27599): (long intergenic non-protein coding RNA 908)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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
LINC00683	ENST00000583578.6	n.326-30982T>C		intron_variant	Intron 2 of 3	3
LINC00683	ENST00000584910.5	n.222-22875T>C		intron_variant	Intron 2 of 2	3
LINC00683	ENST00000651044.1	n.176-30982T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24444 AN: 152122 Hom.: 1982 Cov.: 34

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.161 AC: 24494 AN: 152240 Hom.: 1991 Cov.: 34 AF XY: 0.160 AC XY: 11907 AN XY: 74432

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.176

Alfa AF: 0.154 Hom.: 1196

Bravo AF: 0.164

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2174899; hg19: chr18-74291820;