dbSNP rs6115686: TMEM239:c.*667C>T (chr20-2817680-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_001167670.3(TMEM239):c.*667C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 153,524 control chromosomes in the GnomAD database, including 1,295 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 0.080 ( 1295 hom., cov: 33)

Exomes 𝑓: 0.0055 ( 0 hom. )

Consequence

TMEM239
NM_001167670.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.148

Publications

1 publications found

Variant links:

Genes affected

TMEM239 (HGNC:40044): (transmembrane protein 239) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM239 links:

ENSG00000241690 (HGNC:):

ENSG00000241690 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM239	NM_001167670.3 link	c.*667C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000380585.2	NP_001161142.1	Q8WW34-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TMEM239	ENST00000380585.2 link	c.*667C>T	3_prime_UTR_variant	Exon 2 of 2	1	NM_001167670.3	ENSP00000369959.1	Q8WW34-2
ENSG00000241690	ENST00000380593.4 link	c.*632C>T	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000369967.4	Q6ZPB1
TMEM239	ENST00000361033.1 link	c.*667C>T	3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000354312.1	Q8WW34-1

Frequencies

GnomAD3 genomes

AF:

0.0803

AC:

12217

AN:

152134

Hom.:

1296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.235

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0335

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0138

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00413

Gnomad OTH

AF:

0.0626

GnomAD4 exome

AF:

0.00550

AC:

AN:

1272

Hom.:

Cov.:

AF XY:

0.00831

AC XY:

AN XY:

602

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00676

AC:

AN:

148

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.375

AC:

AN:

South Asian (SAS)

AF:

0.143

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1046

Other (OTH)

AF:

0.0263

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0803

AC:

12225

AN:

152252

Hom.:

1295

Cov.:

AF XY:

0.0818

AC XY:

6089

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.235

AC:

9742

AN:

41510

American (AMR)

AF:

0.0334

AC:

511

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00461

AC:

AN:

3470

East Asian (EAS)

AF:

0.170

AC:

880

AN:

5176

South Asian (SAS)

AF:

0.106

AC:

512

AN:

4828

European-Finnish (FIN)

AF:

0.0138

AC:

147

AN:

10622

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00413

AC:

281

AN:

68032

Other (OTH)

AF:

0.0624

AC:

132

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

506

1013

1519

2026

2532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<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:

0.0379

Hom.:

200

Bravo

AF:

0.0885

Asia WGS

AF:

0.147

AC:

510

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.1

(source)

DANN

Benign

0.69

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over