chr11-111106850-A-C

Variant names:

• chr11-111106850-A-C
• rs224770
• ENST00000636877.1:n.838-14539T>G

Variant summary

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

The ENST00000636877.1(LINC02550):​n.838-14539T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,974 control chromosomes in the GnomAD database, including 11,000 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 0.37 (11000 hom., cov: 32)
• Consequence: LINC02550 ENST00000636877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727
• Publications: 2 publications found

Genes affected

LINC02550 (HGNC:53585): (long intergenic non-protein coding RNA 2550)

ENSG00000270202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.456 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
LINC02550	ENST00000636877.1	n.838-14539T>G		intron_variant	Intron 3 of 3	5
LINC02550	ENST00000783537.1	n.387+13004T>G		intron_variant	Intron 1 of 1
ENSG00000270202	ENST00000604639.1	n.*210T>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56919 AN: 151856 Hom.: 10967 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.375 AC: 56986 AN: 151974 Hom.: 11000 Cov.: 32 AF XY: 0.376 AC XY: 27903 AN XY: 74298

African (AFR) AF: 0.437 AC: 18103 AN: 41460

American (AMR) AF: 0.465 AC: 7090 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1846 AN: 5154

South Asian (SAS) AF: 0.316 AC: 1519 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2901 AN: 10578

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23391 AN: 67934

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.368 Hom.: 12708

Bravo AF: 0.395

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs224770; hg19: chr11-110977574;