dbSNP rs1059804: TMEM184B:c.*1940T>A (chr22-38219529-A-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_012264.5(TMEM184B):c.*1940T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 874,882 control chromosomes in the GnomAD database, including 194,548 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.75 ( 41825 hom., cov: 29)

Exomes 𝑓: 0.70 ( 152723 hom. )

Consequence

TMEM184B
NM_012264.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0790

Publications

7 publications found

Variant links:

Genes affected

TMEM184B (HGNC:1310): (transmembrane protein 184B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM184B links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_012264.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.57).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012264.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM184B	NM_012264.5	MANE Select	c.*1940T>A	3_prime_UTR	Exon 9 of 9	NP_036396.2	Q9Y519
TMEM184B	NM_001195071.1		c.*1940T>A	3_prime_UTR	Exon 9 of 9	NP_001182000.1	Q9Y519
TMEM184B	NM_001195072.2		c.*1940T>A	3_prime_UTR	Exon 10 of 10	NP_001182001.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM184B	ENST00000361906.8	TSL:1 MANE Select	c.*1940T>A	3_prime_UTR	Exon 9 of 9	ENSP00000355210.3	Q9Y519
TMEM184B	ENST00000361684.8	TSL:1	c.*1940T>A	3_prime_UTR	Exon 9 of 9	ENSP00000354441.4	Q9Y519
TMEM184B	ENST00000436674.5	TSL:1	n.*3046T>A	non_coding_transcript_exon	Exon 10 of 10	ENSP00000413085.1	F2Z397

Frequencies

GnomAD3 genomes

AF:

0.747

AC:

111874

AN:

149826

Hom.:

41795

Cov.:

show subpopulations

Gnomad AFR

AF:

0.808

Gnomad AMI

AF:

0.516

Gnomad AMR

AF:

0.741

Gnomad ASJ

AF:

0.711

Gnomad EAS

AF:

0.736

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.760

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.722

Gnomad OTH

AF:

0.731

GnomAD4 exome

AF:

0.696

AC:

504785

AN:

724966

Hom.:

152723

Cov.:

AF XY:

0.697

AC XY:

233228

AN XY:

334716

show subpopulations

African (AFR)

AF:

0.747

AC:

10266

AN:

13734

American (AMR)

AF:

0.715

AC:

621

AN:

868

Ashkenazi Jewish (ASJ)

AF:

0.693

AC:

3120

AN:

4502

East Asian (EAS)

AF:

0.709

AC:

2195

AN:

3094

South Asian (SAS)

AF:

0.661

AC:

9237

AN:

13974

European-Finnish (FIN)

AF:

0.733

AC:

456

AN:

622

Middle Eastern (MID)

AF:

0.697

AC:

990

AN:

1420

European-Non Finnish (NFE)

AF:

0.696

AC:

461478

AN:

663124

Other (OTH)

AF:

0.695

AC:

16422

AN:

23628

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

10503

21006

31510

42013

52516

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17166

34332

51498

68664

85830

<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:

0.747

AC:

111950

AN:

149916

Hom.:

41825

Cov.:

AF XY:

0.746

AC XY:

54539

AN XY:

73152

show subpopulations

African (AFR)

AF:

0.808

AC:

32935

AN:

40774

American (AMR)

AF:

0.742

AC:

11205

AN:

15104

Ashkenazi Jewish (ASJ)

AF:

0.711

AC:

2448

AN:

3444

East Asian (EAS)

AF:

0.737

AC:

3766

AN:

5112

South Asian (SAS)

AF:

0.663

AC:

3162

AN:

4768

European-Finnish (FIN)

AF:

0.760

AC:

7706

AN:

10144

Middle Eastern (MID)

AF:

0.645

AC:

187

AN:

290

European-Non Finnish (NFE)

AF:

0.722

AC:

48566

AN:

67302

Other (OTH)

AF:

0.727

AC:

1510

AN:

2076

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1443

2886

4329

5772

7215

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

836

1672

2508

3344

4180

<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:

0.718

Hom.:

4049

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

0.13

(source)

DANN

Benign

0.73

PhyloP100

-0.079

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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