Variant 15-42236478-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015497.5(TMEM87A):c.869-59G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 1,398,526 control chromosomes in the GnomAD database, including 408,524 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 0.60 ( 33011 hom., cov: 32)

Exomes 𝑓: 0.77 ( 375513 hom. )

Consequence

TMEM87A
NM_015497.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.704

Variant links:

Genes affected

TMEM87A (HGNC:24522): (transmembrane protein 87A) Involved in retrograde transport, endosome to Golgi. Located in Golgi cisterna membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM87A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM87A	NM_015497.5 linkuse as main transcript	c.869-59G>A		intron_variant		ENST00000389834.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM87A	ENST00000389834.9 linkuse as main transcript	c.869-59G>A		intron_variant		2	NM_015497.5	P4	Q8NBN3-1

Frequencies

GnomAD3 genomes

AF:

0.596

AC:

90557

AN:

151952

Hom.:

33021

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.885

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.710

Gnomad EAS

AF:

0.813

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.781

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.804

Gnomad OTH

AF:

0.641

GnomAD4 exome

AF:

0.766

AC:

955099

AN:

1246456

Hom.:

375513

AF XY:

0.767

AC XY:

483710

AN XY:

630690

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.490

Gnomad4 ASJ exome

AF:

0.734

Gnomad4 EAS exome

AF:

0.831

Gnomad4 SAS exome

AF:

0.673

Gnomad4 FIN exome

AF:

0.790

Gnomad4 NFE exome

AF:

0.806

Gnomad4 OTH exome

AF:

0.735

GnomAD4 genome

AF:

0.595

AC:

90537

AN:

152070

Hom.:

33011

Cov.:

AF XY:

0.597

AC XY:

44385

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.576

Gnomad4 ASJ

AF:

0.710

Gnomad4 EAS

AF:

0.813

Gnomad4 SAS

AF:

0.667

Gnomad4 FIN

AF:

0.781

Gnomad4 NFE

AF:

0.804

Gnomad4 OTH

AF:

0.645

Alfa

AF:

0.754

Hom.:

67143

Bravo

AF:

0.561

Asia WGS

AF:

0.699

AC:

2432

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.52

DANN

Benign

0.29

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