2-19494045-A-G

Variant names:

• chr2-19494045-A-G
• rs10495696
• ENST00000641680.1:n.530+5556A>G

Variant summary

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

The ENST00000641680.1(LINC01808):​n.530+5556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,250 control chromosomes in the GnomAD database, including 634 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 0.084 (634 hom., cov: 33)
• Consequence: LINC01808 ENST00000641680.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 3 publications found

Genes affected

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

ENSG00000306962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01808	NR_183418.1	n.605+5556A>G		intron_variant	Intron 5 of 5
LINC01808	NR_183420.1	n.544+5556A>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01808	ENST00000641680.1	n.530+5556A>G		intron_variant	Intron 5 of 5
LINC01808	ENST00000641932.1	n.1194+5556A>G		intron_variant	Intron 6 of 6
LINC01808	ENST00000657829.1	n.649+5556A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12752 AN: 152132 Hom.: 619 Cov.: 33

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0935

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0841 AC: 12797 AN: 152250 Hom.: 634 Cov.: 33 AF XY: 0.0862 AC XY: 6417 AN XY: 74436

African (AFR) AF: 0.0975 AC: 4053 AN: 41548

American (AMR) AF: 0.155 AC: 2366 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 147 AN: 3472

East Asian (EAS) AF: 0.0527 AC: 273 AN: 5178

South Asian (SAS) AF: 0.0379 AC: 183 AN: 4828

European-Finnish (FIN) AF: 0.0935 AC: 992 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0670 AC: 4559 AN: 68012

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.0694 Hom.: 469

Bravo AF: 0.0916

Asia WGS AF: 0.0660 AC: 230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.47
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10495696; hg19: chr2-19693806;