Variant 7-1547017-A-AGCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_001097620.2(TMEM184A):c.1176_1177insGGC(p.Gly392dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 1,595,860 control chromosomes in the GnomAD database, including 231,447 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.55 ( 22810 hom., cov: 0)

Exomes 𝑓: 0.54 ( 208637 hom. )

Consequence

TMEM184A
NM_001097620.2 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.07

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001097620.2. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 7-1547017-A-AGCC is Benign according to our data. Variant chr7-1547017-A-AGCC is described in ClinVar as [Benign]. Clinvar id is 768127.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM184A	NM_001097620.2 linkuse as main transcript	c.1176_1177insGGC	p.Gly392dup	inframe_insertion	9/9	ENST00000297477.10	NP_001091089.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TMEM184A	ENST00000297477.10 linkuse as main transcript	c.1176_1177insGGC	p.Gly392dup	inframe_insertion	9/9	1	NM_001097620.2	ENSP00000297477	P1
TMEM184A	ENST00000468535.5 linkuse as main transcript	n.2054_2055insGGC		non_coding_transcript_exon_variant	6/6	2
TMEM184A	ENST00000319018.12 linkuse as main transcript	c.599_600insGGC		3_prime_UTR_variant, NMD_transcript_variant	8/8	5		ENSP00000326348

Frequencies

GnomAD3 genomes

AF:

0.548

AC:

82887

AN:

151210

Hom.:

22810

Cov.:

show subpopulations

Gnomad AFR

AF:

0.555

Gnomad AMI

AF:

0.678

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.651

Gnomad SAS

AF:

0.539

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.537

Gnomad OTH

AF:

0.549

GnomAD3 exomes

AF:

0.535

AC:

119341

AN:

223240

Hom.:

31732

AF XY:

0.537

AC XY:

66162

AN XY:

123126

show subpopulations

Gnomad AFR exome

AF:

0.541

Gnomad AMR exome

AF:

0.473

Gnomad ASJ exome

AF:

0.453

Gnomad EAS exome

AF:

0.633

Gnomad SAS exome

AF:

0.534

Gnomad FIN exome

AF:

0.618

Gnomad NFE exome

AF:

0.531

Gnomad OTH exome

AF:

0.550

GnomAD4 exome

AF:

0.537

AC:

775216

AN:

1444534

Hom.:

208637

Cov.:

AF XY:

0.537

AC XY:

386058

AN XY:

718592

show subpopulations

Gnomad4 AFR exome

AF:

0.556

Gnomad4 AMR exome

AF:

0.474

Gnomad4 ASJ exome

AF:

0.458

Gnomad4 EAS exome

AF:

0.656

Gnomad4 SAS exome

AF:

0.537

Gnomad4 FIN exome

AF:

0.626

Gnomad4 NFE exome

AF:

0.533

Gnomad4 OTH exome

AF:

0.530

GnomAD4 genome

AF:

0.548

AC:

82916

AN:

151326

Hom.:

22810

Cov.:

AF XY:

0.548

AC XY:

40517

AN XY:

73930

show subpopulations

Gnomad4 AFR

AF:

0.555

Gnomad4 AMR

AF:

0.515

Gnomad4 ASJ

AF:

0.454

Gnomad4 EAS

AF:

0.650

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.614

Gnomad4 NFE

AF:

0.537

Gnomad4 OTH

AF:

0.544

Alfa

AF:

0.444

Hom.:

1910

Asia WGS

AF:

0.555

AC:

1927

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over