Variant rs3741324 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032780.4(TMEM25):c.*540G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,016,926 control chromosomes in the GnomAD database, including 11,554 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 0.16 ( 2453 hom., cov: 32)

Exomes 𝑓: 0.14 ( 9101 hom. )

Consequence

TMEM25
NM_032780.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.494

Variant links:

Genes affected

TMEM25 (HGNC:25890): (transmembrane protein 25) Predicted to be involved in negative regulation of excitatory postsynaptic potential and regulation of protein stability. Predicted to be located in late endosome and lysosome. [provided by Alliance of Genome Resources, Apr 2022]

TMEM25 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM25	NM_032780.4 linkuse as main transcript	c.*540G>A		3_prime_UTR_variant	9/9	ENST00000313236.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM25	ENST00000313236.10 linkuse as main transcript	c.*540G>A		3_prime_UTR_variant	9/9	1	NM_032780.4	P1	Q86YD3-1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24505

AN:

151918

Hom.:

2456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.0962

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.493

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.151

GnomAD4 exome

AF:

0.138

AC:

119110

AN:

864890

Hom.:

9101

Cov.:

AF XY:

0.138

AC XY:

55471

AN XY:

400698

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.0757

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.484

Gnomad4 SAS exome

AF:

0.328

Gnomad4 FIN exome

AF:

0.148

Gnomad4 NFE exome

AF:

0.129

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.161

AC:

24518

AN:

152036

Hom.:

2453

Cov.:

AF XY:

0.166

AC XY:

12308

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.0960

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.493

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.132

Hom.:

1150

Bravo

AF:

0.155

Asia WGS

AF:

0.424

AC:

1472

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.78

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over