rs1499447

Variant names:

• chr8-136970046-C-T
• rs1499447
• ENST00000521034.1:n.304+8195C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000521034.1(LINC02055):​n.304+8195C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,212 control chromosomes in the GnomAD database, including 68 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 0.024 (68 hom., cov: 32)
• Consequence: LINC02055 ENST00000521034.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 0 publications found

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0237 (3612/152212) while in subpopulation NFE AF = 0.0349 (2373/68010). AF 95% confidence interval is 0.0337. There are 68 homozygotes in GnomAd4. There are 1681 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 68 gene

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
LINC02055	ENST00000521034.1	n.304+8195C>T		intron_variant	Intron 3 of 3	5
LINC02055	ENST00000649576.1	n.676+8195C>T		intron_variant	Intron 6 of 8
LINC02055	ENST00000837562.1	n.264+8195C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3616 AN: 152094 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.00693

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00963

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0237 AC: 3612 AN: 152212 Hom.: 68 Cov.: 32 AF XY: 0.0226 AC XY: 1681 AN XY: 74420

African (AFR) AF: 0.00691 AC: 287 AN: 41536

American (AMR) AF: 0.0278 AC: 425 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 226 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4824

European-Finnish (FIN) AF: 0.00963 AC: 102 AN: 10592

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

European-Non Finnish (NFE) AF: 0.0349 AC: 2373 AN: 68010

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0327 Hom.: 141

Bravo AF: 0.0245

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1499447; hg19: chr8-137982289;