dbSNP rs7811444: TMEM184A:c.-1+53T>C (chr7-1556560-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000431208.1(TMEM184A):c.1-1076T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,170 control chromosomes in the GnomAD database, including 8,379 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 0.31 ( 8373 hom., cov: 33)

Exomes 𝑓: 0.33 ( 6 hom. )

Consequence

TMEM184A
ENST00000431208.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.659

Publications

3 publications found

Variant links:

Genes affected

TMEM184A (HGNC:28797): (transmembrane protein 184A) Predicted to enable heparin binding activity. Predicted to act upstream of or within germ-line sex determination; regulation of protein localization; and regulation of secretion. Predicted to be located in cytoplasmic vesicle; perinuclear region of cytoplasm; and plasma membrane. Predicted to be active in early endosome membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM184A links:

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new If you want to explore the variant's impact on the transcript ENST00000431208.1, 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431208.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TMEM184A	ENST00000910336.1		c.-1+53T>C	intron	N/A	ENSP00000580395.1
TMEM184A	ENST00000431208.1	TSL:4	c.1-1076T>C	intron	N/A	ENSP00000403499.1	C9JDD9
TMEM184A	ENST00000421923.5	TSL:5	n.1-1076T>C	intron	N/A	ENSP00000413955.1	F8WEG1

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46779

AN:

151958

Hom.:

8344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.305

GnomAD4 exome

AF:

0.330

AC:

AN:

Hom.:

AF XY:

0.328

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.304

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.583

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.308

AC:

46862

AN:

152076

Hom.:

8373

Cov.:

AF XY:

0.301

AC XY:

22352

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.490

AC:

20305

AN:

41464

American (AMR)

AF:

0.302

AC:

4618

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

759

AN:

3470

East Asian (EAS)

AF:

0.107

AC:

554

AN:

5164

South Asian (SAS)

AF:

0.186

AC:

900

AN:

4828

European-Finnish (FIN)

AF:

0.175

AC:

1859

AN:

10600

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

16995

AN:

67948

Other (OTH)

AF:

0.301

AC:

635

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1592

3185

4777

6370

7962

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<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:

0.269

Hom.:

7651

Bravo

AF:

0.327

Asia WGS

AF:

0.160

AC:

558

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.42

PhyloP100

-0.66

PromoterAI

-0.022

Neutral

(source)

Splicing

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

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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