ENST00000555433.2:n.220+11767C>T

Variant names:

• chr14-44520496-C-T
• rs1118997
• ENST00000555433.2:n.220+11767C>T

Variant summary

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

The ENST00000555433.2(ENSG00000258747):​n.220+11767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,980 control chromosomes in the GnomAD database, including 3,381 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 0.19 (3381 hom., cov: 32)
• Consequence: ENSG00000258747 ENST00000555433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 2 publications found

Genes affected

ENSG00000258747 (HGNC:):

LINC02277 (HGNC:53193): (long intergenic non-protein coding RNA 2277)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370473	NR_135257.1	n.139+11767C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258747	ENST00000555433.2	n.220+11767C>T		intron_variant	Intron 2 of 2	2
ENSG00000258747	ENST00000556228.1	n.229+11265C>T		intron_variant	Intron 1 of 1	3
LINC02277	ENST00000557721.2	n.108-75674G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28660 AN: 151862 Hom.: 3366 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.189 AC: 28704 AN: 151980 Hom.: 3381 Cov.: 32 AF XY: 0.194 AC XY: 14426 AN XY: 74312

African (AFR) AF: 0.278 AC: 11512 AN: 41430

American (AMR) AF: 0.268 AC: 4090 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3468

East Asian (EAS) AF: 0.387 AC: 1999 AN: 5168

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4816

European-Finnish (FIN) AF: 0.107 AC: 1129 AN: 10550

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7491 AN: 67974

Other (OTH) AF: 0.183 AC: 384 AN: 2100

Alfa AF: 0.154 Hom.: 293

Bravo AF: 0.205

Asia WGS AF: 0.334 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.50
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1118997; hg19: chr14-44989699;