chr14-100824126-C-A

Variant names:

• chr14-100824126-C-A
• rs11627993
• ENST00000741306.1:n.723C>A

Variant summary

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

The ENST00000741306.1(ENSG00000296722):​n.723C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,144 control chromosomes in the GnomAD database, including 6,870 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 0.28 (6870 hom., cov: 33)
• Consequence: ENSG00000296722 ENST00000741306.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 4 publications found

Genes affected

ENSG00000296722 (HGNC:):

MEG3 (HGNC:14575): (maternally expressed 3) This gene is a maternally expressed imprinted gene. Multiple alternatively spliced transcript variants have been transcribed from this gene and all of them are long non-coding RNAs (lncRNAs). This gene is expressed in many normal tissues, but its expression is lost in multiple cancer cell lines of various tissue origins. It inhibits tumor cell proliferation in vitro. It also interacts with the tumor suppressor p53, and regulates p53 target gene expression. Its deletion enhances angiogenesis in vivo. Many experimental evidences demonstrate that this gene is a lncRNA tumor suppressor. [provided by RefSeq, Mar 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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
ENSG00000296722	ENST00000741306.1	n.723C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296722	ENST00000741307.1	n.911C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296722	ENST00000741308.1	n.711C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43211 AN: 152026 Hom.: 6864 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.284 AC: 43260 AN: 152144 Hom.: 6870 Cov.: 33 AF XY: 0.295 AC XY: 21942 AN XY: 74370

African (AFR) AF: 0.181 AC: 7506 AN: 41548

American (AMR) AF: 0.389 AC: 5944 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3472

East Asian (EAS) AF: 0.582 AC: 2993 AN: 5140

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4810

European-Finnish (FIN) AF: 0.346 AC: 3662 AN: 10592

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18885 AN: 67974

Other (OTH) AF: 0.309 AC: 652 AN: 2110

Alfa AF: 0.148 Hom.: 303

Bravo AF: 0.288

Asia WGS AF: 0.492 AC: 1715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11627993; hg19: chr14-101290463;