rs10512889

Variant names:

• chr5-6868809-C-T
• rs10512889
• ENST00000510622.2:n.130+176C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000510622.2(LINC02196):​n.130+176C>T variant causes a intron 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 ENST00000510622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941
• Publications: 4 publications found

Genes affected

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

LOC105374642 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374642	NR_188250.1	n.285-1934C>T		intron_variant	Intron 1 of 2
LOC105374642	NR_188251.1	n.285-17617C>T		intron_variant	Intron 1 of 1
LOC105374642	NR_188252.1	n.87+176C>T		intron_variant	Intron 1 of 2
LOC105374642	NR_188253.1	n.87+176C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02196	ENST00000510622.2	n.130+176C>T		intron_variant	Intron 1 of 2	5
LINC02196	ENST00000648809.1	n.172+29178C>T		intron_variant	Intron 1 of 5
LINC02196	ENST00000655466.2	n.93+176C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.514 AC: 17532 AN: 34126 Hom.: 1528 Cov.: 0

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

African (AFR) AF: 0.443 AC: 2734 AN: 6166

American (AMR) AF: 0.559 AC: 2566 AN: 4594

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 629 AN: 1128

East Asian (EAS) AF: 0.253 AC: 44 AN: 174

South Asian (SAS) AF: 0.493 AC: 402 AN: 816

European-Finnish (FIN) AF: 0.490 AC: 861 AN: 1756

Middle Eastern (MID) AF: 0.500 AC: 30 AN: 60

European-Non Finnish (NFE) AF: 0.528 AC: 9857 AN: 18676

Other (OTH) AF: 0.514 AC: 224 AN: 436

Alfa AF: 0.165 Hom.: 1359

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
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs10512889; hg19: chr5-6868922;