rs10512991

chr5-8883253-A-G

Variant summary

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

The ENST00000651480.1(LINC02199):n.364+2202A>G 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 0.0202 in 152,322 control chromosomes in the GnomAD database, including 37 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 0.020 (37 hom., cov: 32)
• Consequence: LINC02199 ENST00000651480.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

Genes affected

LINC02199 (HGNC:53065): (long intergenic non-protein coding RNA 2199)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0202 (3084/152322) while in subpopulation EAS AF= 0.0442 (229/5182). AF 95% confidence interval is 0.0395. There are 37 homozygotes in gnomad4. There are 1540 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02199	ENST00000651480.1	n.364+2202A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0202 AC: 3074 AN: 152206 Hom.: 35 Cov.: 32

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.0233

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0202 AC: 3084 AN: 152322 Hom.: 37 Cov.: 32 AF XY: 0.0207 AC XY: 1540 AN XY: 74476

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0190

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0442

Gnomad4 SAS AF: 0.0195

Gnomad4 FIN AF: 0.0233

Gnomad4 NFE AF: 0.0177

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0182 Hom.: 4

Bravo AF: 0.0199

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.4
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512991; hg19: chr5-8883365;