rs1499447

Positions:

• chr8-136970046-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000521034.1(LINC02055):​n.304+8195C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 68 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02055	ENST00000521034.1	n.304+8195C>T		intron_variant, non_coding_transcript_variant		5
LINC02055	ENST00000649576.1	n.676+8195C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00691

Gnomad4 AMR AF: 0.0278

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.00963

Gnomad4 NFE AF: 0.0349

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0308 Hom.: 35

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1499447; hg19: chr8-137982289;