14-100831954-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000452120.7(MEG3):​n.3130T>G 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 0.00791 in 152,034 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0079 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MEG3
ENST00000452120.7 non_coding_transcript_exon

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.232
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 14-100831954-T-G is Benign according to our data. Variant chr14-100831954-T-G is described in ClinVar as [Benign]. Clinvar id is 2644540.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MEG3NR_002766.2 linkuse as main transcriptn.1049+420T>G intron_variant
MEG3NR_003530.2 linkuse as main transcriptn.1049+420T>G intron_variant
MEG3NR_003531.3 linkuse as main transcriptn.1025+420T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MEG3ENST00000429159.6 linkuse as main transcriptn.936-558T>G intron_variant 1
MEG3ENST00000451743.6 linkuse as main transcriptn.1031+420T>G intron_variant 1
MEG3ENST00000521404.5 linkuse as main transcriptn.917+2205T>G intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.00791
AC:
1202
AN:
151916
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00256
Gnomad AMI
AF:
0.0186
Gnomad AMR
AF:
0.00616
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00104
Gnomad FIN
AF:
0.00436
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0134
Gnomad OTH
AF:
0.00814
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
10
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
4
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.00791
AC:
1202
AN:
152034
Hom.:
9
Cov.:
32
AF XY:
0.00721
AC XY:
536
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.00256
Gnomad4 AMR
AF:
0.00615
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.00436
Gnomad4 NFE
AF:
0.0134
Gnomad4 OTH
AF:
0.00806
Alfa
AF:
0.0109
Hom.:
1
Bravo
AF:
0.00812
Asia WGS
AF:
0.00173
AC:
7
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2024MEG3: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.7
DANN
Benign
0.75

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs72698763; hg19: chr14-101298291; API