rs224770

Positions:

• chr11-111106850-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636877.1(LINC02550):​n.838-14539T>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 0.375 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.727

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02550	ENST00000636877.1	n.838-14539T>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.370

Alfa AF: 0.359 Hom.: 6185

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224770; hg19: chr11-110977574;