chr13-30921021-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_032849.4(MEDAG):​c.396G>A​(p.Thr132=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00226 in 1,613,278 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0023 ( 7 hom. )

Consequence

MEDAG
NM_032849.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.31
Variant links:
Genes affected
MEDAG (HGNC:25926): (mesenteric estrogen dependent adipogenesis) Predicted to be involved in positive regulation of fat cell differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
TEX26-AS1 (HGNC:42784): (TEX26 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 13-30921021-G-A is Benign according to our data. Variant chr13-30921021-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2643712.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.31 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MEDAGNM_032849.4 linkuse as main transcriptc.396G>A p.Thr132= synonymous_variant 3/5 ENST00000380482.9
TEX26-AS1NR_038287.1 linkuse as main transcriptn.1437+9780C>T intron_variant, non_coding_transcript_variant
MEDAGXM_017020801.2 linkuse as main transcriptc.-58G>A 5_prime_UTR_variant 2/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MEDAGENST00000380482.9 linkuse as main transcriptc.396G>A p.Thr132= synonymous_variant 3/51 NM_032849.4 P1Q5VYS4-1
TEX26-AS1ENST00000585870.6 linkuse as main transcriptn.1437+9780C>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.00172
AC:
261
AN:
152172
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000386
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000523
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00528
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00262
Gnomad OTH
AF:
0.000957
GnomAD3 exomes
AF:
0.00216
AC:
541
AN:
250652
Hom.:
3
AF XY:
0.00219
AC XY:
296
AN XY:
135400
show subpopulations
Gnomad AFR exome
AF:
0.000185
Gnomad AMR exome
AF:
0.000522
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00476
Gnomad NFE exome
AF:
0.00354
Gnomad OTH exome
AF:
0.00245
GnomAD4 exome
AF:
0.00232
AC:
3387
AN:
1460988
Hom.:
7
Cov.:
30
AF XY:
0.00228
AC XY:
1656
AN XY:
726736
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
Gnomad4 AMR exome
AF:
0.000560
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00640
Gnomad4 NFE exome
AF:
0.00258
Gnomad4 OTH exome
AF:
0.00230
GnomAD4 genome
AF:
0.00171
AC:
261
AN:
152290
Hom.:
0
Cov.:
33
AF XY:
0.00173
AC XY:
129
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.000385
Gnomad4 AMR
AF:
0.000523
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00528
Gnomad4 NFE
AF:
0.00262
Gnomad4 OTH
AF:
0.000947
Alfa
AF:
0.00222
Hom.:
3
Bravo
AF:
0.00136
Asia WGS
AF:
0.000577
AC:
3
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2022MEDAG: BP4, BP7, BS2; TEX26-AS1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.65
CADD
Benign
0.27
DANN
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs41291239; hg19: chr13-31495158; API