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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001167670.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM239	NM_001167670.3	MANE Select	c.*667C>T		3_prime_UTR	Exon 2 of 2	NP_001161142.1	Q8WW34-2
	TMEM239	NM_001318207.1		c.*667C>T		3_prime_UTR	Exon 2 of 2	NP_001305136.1	Q8WW34-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM239	ENST00000380585.2	TSL:1 MANE Select	c.*667C>T	3_prime_UTR	Exon 2 of 2	ENSP00000369959.1	Q8WW34-2
ENSG00000241690	ENST00000380593.4	TSL:2	c.*632C>T	3_prime_UTR	Exon 3 of 3	ENSP00000369967.4	Q6ZPB1
TMEM239	ENST00000361033.1	TSL:2	c.*667C>T	3_prime_UTR	Exon 2 of 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 v4.9

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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