Variant rs1053051 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_152261.4(TMEM263):c.*2056T>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 0.607 in 151,898 control chromosomes in the GnomAD database, including 29,342 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 0.61 ( 29284 hom., cov: 32)

Exomes 𝑓: 0.52 ( 58 hom. )

Consequence

TMEM263
NM_152261.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Variant links:

Genes affected

TMEM263 (HGNC:28281): (transmembrane protein 263) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM263 links:

MTERF2 (HGNC:30779): (mitochondrial transcription termination factor 2) Enables DNA binding activity. Predicted to be involved in termination of mitochondrial transcription. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

MTERF2 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=-0.62).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM263	NM_152261.4 linkuse as main transcript	c.*2056T>C		3_prime_UTR_variant	4/4	ENST00000280756.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM263	ENST00000280756.9 linkuse as main transcript	c.*2056T>C		3_prime_UTR_variant	4/4	1	NM_152261.4	P1

Frequencies

GnomAD3 genomes

AF:

0.607

AC:

91817

AN:

151348

Hom.:

29235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.592

Gnomad AMR

AF:

0.670

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.637

Gnomad SAS

AF:

0.615

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.558

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.583

GnomAD4 exome

AF:

0.523

AC:

226

AN:

432

Hom.:

Cov.:

AF XY:

0.538

AC XY:

140

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.521

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.607

AC:

91921

AN:

151466

Hom.:

29284

Cov.:

AF XY:

0.611

AC XY:

45234

AN XY:

73998

show subpopulations

Gnomad4 AFR

AF:

0.793

Gnomad4 AMR

AF:

0.670

Gnomad4 ASJ

AF:

0.664

Gnomad4 EAS

AF:

0.638

Gnomad4 SAS

AF:

0.614

Gnomad4 FIN

AF:

0.522

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.580

Alfa

AF:

0.521

Hom.:

35483

Bravo

AF:

0.630

Asia WGS

AF:

0.617

AC:

2140

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.65

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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