Genetic Variant TMEM272:c.202-92G>A (chr13-51817205-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

4 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351003.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM272	NM_001351003.2	MANE Select	c.202-92G>A	intron	N/A	NP_001337932.1	A0A1B0GTI8-1
TMEM272	NM_001351006.2		c.4-92G>A	intron	N/A	NP_001337935.1	A0A1B0GTI8-2
TMEM272	NM_001351005.2		c.-30-92G>A	intron	N/A	NP_001337934.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM272	ENST00000629372.3	TSL:4 MANE Select	c.202-92G>A	intron	N/A	ENSP00000490718.2	A0A1B0GTI8-1
ENSG00000285444	ENST00000642706.1		n.59-3866G>A	intron	N/A	ENSP00000495561.1	A0A2R8Y6I0
TMEM272	ENST00000626362.3	TSL:4	c.119-92G>A	intron	N/A	ENSP00000489719.2	A0A5H1ZRT5

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

African (AFR)

AF:

0.661

AC:

8832

AN:

13364

American (AMR)

AF:

0.744

AC:

17976

AN:

24164

Ashkenazi Jewish (ASJ)

AF:

0.720

AC:

10640

AN:

14770

East Asian (EAS)

AF:

0.411

AC:

12853

AN:

31242

South Asian (SAS)

AF:

0.665

AC:

33057

AN:

49736

European-Finnish (FIN)

AF:

0.694

AC:

21142

AN:

30446

Middle Eastern (MID)

AF:

0.702

AC:

2564

AN:

3652

European-Non Finnish (NFE)

AF:

0.736

AC:

202128

AN:

274574

Other (OTH)

AF:

0.701

AC:

18919

AN:

27002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

5202

10404

15606

20808

26010

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

874

1748

2622

3496

4370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.699

AC:

106092

AN:

151722

Hom.:

37356

Cov.:

AF XY:

0.695

AC XY:

51524

AN XY:

74120

show subpopulations

African (AFR)

AF:

0.655

AC:

27053

AN:

41310

American (AMR)

AF:

0.739

AC:

11287

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.729

AC:

2530

AN:

3470

East Asian (EAS)

AF:

0.469

AC:

2411

AN:

5146

South Asian (SAS)

AF:

0.653

AC:

3135

AN:

4802

European-Finnish (FIN)

AF:

0.684

AC:

7195

AN:

10512

Middle Eastern (MID)

AF:

0.684

AC:

201

AN:

294

European-Non Finnish (NFE)

AF:

0.737

AC:

50020

AN:

67904

Other (OTH)

AF:

0.716

AC:

1505

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1587

3174

4762

6349

7936

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

822

1644

2466

3288

4110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.726

Hom.:

20323

Bravo

AF:

0.702

Asia WGS

AF:

0.608

AC:

2115

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.35

(source)

DANN

Benign

0.48

PhyloP100

-3.2

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over