ENST00000499625.1:n.485-32013T>C

Variant names:

• chr11-22888505-T-C
• rs2429763
• ENST00000499625.1:n.485-32013T>C

Variant summary

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

The ENST00000499625.1(ENSG00000246225):​n.485-32013T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,928 control chromosomes in the GnomAD database, including 4,470 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 0.22 (4470 hom., cov: 32)
• Consequence: ENSG00000246225 ENST00000499625.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 4 publications found

Genes affected

ENSG00000246225 (HGNC:):

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499625.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02718	NR_187205.1		n.493-32013T>C		intron	N/A
	LINC02718	NR_187206.1		n.493-32013T>C		intron	N/A
	LINC02718	NR_187207.1		n.493-32013T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246225	ENST00000499625.1	TSL:5	n.485-32013T>C		intron	N/A
	ENSG00000246225	ENST00000528701.6	TSL:4	n.495-32013T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33649 AN: 151810 Hom.: 4464 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.222 AC: 33674 AN: 151928 Hom.: 4470 Cov.: 32 AF XY: 0.222 AC XY: 16511 AN XY: 74262

African (AFR) AF: 0.381 AC: 15814 AN: 41456

American (AMR) AF: 0.132 AC: 2015 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3466

East Asian (EAS) AF: 0.220 AC: 1140 AN: 5180

South Asian (SAS) AF: 0.260 AC: 1248 AN: 4808

European-Finnish (FIN) AF: 0.143 AC: 1511 AN: 10600

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

European-Non Finnish (NFE) AF: 0.159 AC: 10769 AN: 67834

Other (OTH) AF: 0.207 AC: 437 AN: 2110

Alfa AF: 0.187 Hom.: 1128

Bravo AF: 0.224

Asia WGS AF: 0.276 AC: 960 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2429763; hg19: chr11-22910051;