rs10512889

chr5-6868809-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000648809.1(LINC02196):n.172+29178C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.51 (1528 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: LINC02196 ENST00000648809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941

Genes affected

LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374642	XR_001742496.2	n.521-17617C>T		intron_variant, non_coding_transcript_variant
LOC105374642	XR_925741.3	n.73C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02196	ENST00000648809.1	n.172+29178C>T		intron_variant, non_coding_transcript_variant
	ENST00000655466.1	n.80+176C>T		intron_variant, non_coding_transcript_variant
	ENST00000510622.1	n.75+176C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 17532 AN: 34126 Hom.: 1528 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.516

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.514 AC: 17543 AN: 34156 Hom.: 1528 Cov.: 0 AF XY: 0.510 AC XY: 8357 AN XY: 16376

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.514

Alfa AF: 0.165 Hom.: 1255

Bravo AF: 0.146

Asia WGS AF: 0.0870 AC: 303 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	8.0
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512889; hg19: chr5-6868922;