rs2174899

Variant names:

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

Variant summary

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

The ENST00000583578.6(LINC00908):​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: LINC00908 ENST00000583578.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 4 publications found

Genes affected

LINC00908 (HGNC:27599): (long intergenic non-protein coding RNA 908)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583578.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00908	ENST00000583578.6	TSL:3	n.326-30982T>C		intron	N/A
	LINC00908	ENST00000584910.6	TSL:3	n.325-22875T>C		intron	N/A
	LINC00908	ENST00000651044.1		n.176-30982T>C		intron	N/A

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

African (AFR) AF: 0.180 AC: 7493 AN: 41542

American (AMR) AF: 0.156 AC: 2389 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3472

East Asian (EAS) AF: 0.182 AC: 943 AN: 5172

South Asian (SAS) AF: 0.182 AC: 879 AN: 4832

European-Finnish (FIN) AF: 0.133 AC: 1413 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10111 AN: 67996

Other (OTH) AF: 0.176 AC: 372 AN: 2112

Alfa AF: 0.159 Hom.: 1905

Bravo AF: 0.164

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2174899;

hg19: chr18-74291820;