2-19487388-G-A

Variant names:

• chr2-19487388-G-A
• rs4666488
• ENST00000641932.1:n.945G>A

Variant summary

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

The ENST00000641932.1(LINC01808):​n.945G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 152,180 control chromosomes in the GnomAD database, including 711 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 0.061 (711 hom., cov: 32)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: LINC01808 ENST00000641932.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 2 publications found

Genes affected

LINC01808 (HGNC:52611): (long intergenic non-protein coding RNA 1808)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641932.1. 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
	LINC01808	NR_183418.1		n.484-980G>A		intron	N/A
	LINC01808	NR_183419.1		n.423-980G>A		intron	N/A
	LINC01808	NR_183420.1		n.423-980G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01808	ENST00000641932.1		n.945G>A		non_coding_transcript_exon	Exon 5 of 7
	LINC01808	ENST00000666694.1		n.398G>A		non_coding_transcript_exon	Exon 4 of 5
	LINC01808	ENST00000450628.2	TSL:5	n.355-980G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9246 AN: 152048 Hom.: 713 Cov.: 32

Gnomad AFR AF: 0.0634

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0195

Gnomad OTH AF: 0.0458

GnomAD4 exome AF: 0.0714 AC: 1 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 1 AN: 10

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0608 AC: 9246 AN: 152166 Hom.: 711 Cov.: 32 AF XY: 0.0683 AC XY: 5078 AN XY: 74402

African (AFR) AF: 0.0632 AC: 2621 AN: 41490

American (AMR) AF: 0.110 AC: 1675 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2028 AN: 5168

South Asian (SAS) AF: 0.157 AC: 756 AN: 4812

European-Finnish (FIN) AF: 0.0602 AC: 639 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0195 AC: 1325 AN: 68016

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0350 Hom.: 100

Bravo AF: 0.0638

Asia WGS AF: 0.240 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	8.8
DANN	Benign	0.85
PhyloP100		-0.15

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: rs4666488;

hg19: chr2-19687149;