Genetic Variant TMEM184A:c.1-1076T>C (chr7-1556560-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM184A	ENST00000431208.1 link	c.1-1076T>C		intron_variant	Intron 1 of 3	4		ENSP00000403499.1		C9JDD9
TMEM184A	ENST00000421923.5 link	n.1-1076T>C		intron_variant	Intron 1 of 5	5		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

Gnomad4 AFR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.400

Gnomad4 NFE exome

AF:

0.304

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.308

AC:

46862

AN:

152076

Hom.:

8373

Cov.:

AF XY:

0.301

AC XY:

22352

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.490

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.186

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.250

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.258

Hom.:

5279

Bravo

AF:

0.327

Asia WGS

AF:

0.160

AC:

558

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

DANN

Benign

0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over