Variant 11-61367060-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000542946.2(TMEM138):c.*826T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,146 control chromosomes in the GnomAD database, including 45,716 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 0.74 ( 45708 hom., cov: 31)

Exomes 𝑓: 0.86 ( 8 hom. )

Consequence

TMEM138
ENST00000542946.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.466

Variant links:

Genes affected

TMEM138 (HGNC:26944): (transmembrane protein 138) This gene encodes a multi-pass transmembrane protein. Reduced expression of this gene in mouse fibroblasts causes short cilia and failure of ciliogenesis. Expression of this gene is tightly coordinated with expression of the neighboring gene TMEM216. Mutations in this gene are associated with the autosomal recessive neurodevelopmental disorder Joubert Syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

TMEM138 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM138	NM_016464.5 link	c.300+844T>C		intron_variant		ENST00000278826.11	NP_057548.1	Q9NPI0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM138	ENST00000278826.11 link	c.300+844T>C		intron_variant		1	NM_016464.5	ENSP00000278826.5		Q9NPI0-1

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113234

AN:

152006

Hom.:

45711

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.912

Gnomad AMR

AF:

0.850

Gnomad ASJ

AF:

0.903

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.834

Gnomad FIN

AF:

0.895

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.870

Gnomad OTH

AF:

0.792

GnomAD4 exome

AF:

0.864

AC:

AN:

Hom.:

Cov.:

AF XY:

0.929

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.850

GnomAD4 genome

AF:

0.744

AC:

113246

AN:

152124

Hom.:

45708

Cov.:

AF XY:

0.750

AC XY:

55797

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.399

Gnomad4 AMR

AF:

0.851

Gnomad4 ASJ

AF:

0.903

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.835

Gnomad4 FIN

AF:

0.895

Gnomad4 NFE

AF:

0.870

Gnomad4 OTH

AF:

0.786

Alfa

AF:

0.844

Hom.:

54005

Bravo

AF:

0.728

Asia WGS

AF:

0.837

AC:

2910

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.7

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