Variant 13-51817205-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_001351003.2(TMEM272):c.202-92G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 620,672 control chromosomes in the GnomAD database, including 154,034 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 0.70 ( 37356 hom., cov: 30)

Exomes 𝑓: 0.70 ( 116678 hom. )

Consequence

TMEM272
NM_001351003.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.22

Variant links:

Genes affected

TMEM272 (HGNC:26737): (transmembrane protein 272) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM272 links:

ENSG00000285444 (HGNC:):

ENSG00000285444 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM272	NM_001351003.2 linkuse as main transcript	c.202-92G>A		intron_variant		ENST00000629372.3	NP_001337932.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
TMEM272	ENST00000629372.3 linkuse as main transcript	c.202-92G>A	intron_variant	4	NM_001351003.2	ENSP00000490718.2	A0A1B0GTI8-1
ENSG00000285444	ENST00000642706.1 linkuse as main transcript	n.59-3866G>A	intron_variant			ENSP00000495561.1	A0A2R8Y6I0
TMEM272	ENST00000626362.3 linkuse as main transcript	c.119-92G>A	intron_variant	4		ENSP00000489719.2	A0A5H1ZRT5
TMEM272	ENST00000627246.3 linkuse as main transcript	c.59-92G>A	intron_variant	2		ENSP00000490137.2	A0A5H1ZRT8

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

106031

AN:

151600

Hom.:

37340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.828

Gnomad AMR

AF:

0.740

Gnomad ASJ

AF:

0.729

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.651

Gnomad FIN

AF:

0.684

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.737

Gnomad OTH

AF:

0.718

GnomAD4 exome

AF:

0.700

AC:

328111

AN:

468950

Hom.:

116678

AF XY:

0.698

AC XY:

172936

AN XY:

247588

show subpopulations

Gnomad4 AFR exome

AF:

0.661

Gnomad4 AMR exome

AF:

0.744

Gnomad4 ASJ exome

AF:

0.720

Gnomad4 EAS exome

AF:

0.411

Gnomad4 SAS exome

AF:

0.665

Gnomad4 FIN exome

AF:

0.694

Gnomad4 NFE exome

AF:

0.736

Gnomad4 OTH exome

AF:

0.701

GnomAD4 genome

AF:

0.699

AC:

106092

AN:

151722

Hom.:

37356

Cov.:

AF XY:

0.695

AC XY:

51524

AN XY:

74120

show subpopulations

Gnomad4 AFR

AF:

0.655

Gnomad4 AMR

AF:

0.739

Gnomad4 ASJ

AF:

0.729

Gnomad4 EAS

AF:

0.469

Gnomad4 SAS

AF:

0.653

Gnomad4 FIN

AF:

0.684

Gnomad4 NFE

AF:

0.737

Gnomad4 OTH

AF:

0.716

Alfa

AF:

0.726

Hom.:

18046

Bravo

AF:

0.702

Asia WGS

AF:

0.608

AC:

2115

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.35

DANN

Benign

0.48

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.99

Splicing

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