rs10512991

Variant names:

• chr5-8883253-A-G
• rs10512991
• ENST00000651480.1:n.364+2202A>G

Variant summary

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

The ENST00000651480.1(LINC02199):​n.364+2202A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 37 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
LINC02199	ENST00000651480.1	n.364+2202A>G		intron_variant	Intron 2 of 3
LINC02199	ENST00000796093.1	n.413+2202A>G		intron_variant	Intron 3 of 3
LINC02199	ENST00000796095.1	n.326+2202A>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.0190 AC: 788 AN: 41570

American (AMR) AF: 0.0190 AC: 290 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3472

East Asian (EAS) AF: 0.0442 AC: 229 AN: 5182

South Asian (SAS) AF: 0.0195 AC: 94 AN: 4824

European-Finnish (FIN) AF: 0.0233 AC: 247 AN: 10620

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0177 AC: 1206 AN: 68036

Other (OTH) AF: 0.0227 AC: 48 AN: 2116

Alfa AF: 0.0188 Hom.: 40

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10512991; hg19: chr5-8883365;