chr11-104463511-A-G

Variant names:

• chr11-104463511-A-G
• rs11226373
• ENST00000536529.5:n.508-17499T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536529.5(LINC02552):​n.508-17499T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,890 control chromosomes in the GnomAD database, including 1,964 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 0.16 (1964 hom., cov: 32)
• Consequence: LINC02552 ENST00000536529.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 14 publications found

Genes affected

LINC02552 (HGNC:53587): (long intergenic non-protein coding RNA 2552)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

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
LINC02552	ENST00000536529.5	n.508-17499T>C		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23570 AN: 151772 Hom.: 1951 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0934

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.156 AC: 23625 AN: 151890 Hom.: 1964 Cov.: 32 AF XY: 0.155 AC XY: 11506 AN XY: 74228

African (AFR) AF: 0.193 AC: 7993 AN: 41432

American (AMR) AF: 0.0934 AC: 1424 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3468

East Asian (EAS) AF: 0.164 AC: 841 AN: 5116

South Asian (SAS) AF: 0.180 AC: 867 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1918 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9473 AN: 67902

Other (OTH) AF: 0.146 AC: 308 AN: 2110

Alfa AF: 0.143 Hom.: 2802

Bravo AF: 0.151

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.73
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs11226373; hg19: chr11-104334239;