NM_001097620.2:c.1171_1176dupGGCGGC

Variant names:

• chr7-1547017-A-AGCCGCC
• rs112463195
• NM_001097620.2:c.1171_1176dupGGCGGC

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

The NM_001097620.2(TMEM184A):​c.1171_1176dupGGCGGC​(p.Gly392_Ser393insGlyGly) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000564 in 1,596,904 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000042 (0 hom.)
• Consequence: TMEM184A NM_001097620.2 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_001097620.2.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM184A	NM_001097620.2	c.1171_1176dupGGCGGC	p.Gly392_Ser393insGlyGly	conservative_inframe_insertion	Exon 9 of 9	ENST00000297477.10	NP_001091089.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM184A	ENST00000297477.10	c.1171_1176dupGGCGGC	p.Gly392_Ser393insGlyGly	conservative_inframe_insertion	Exon 9 of 9	1	NM_001097620.2	ENSP00000297477.4
TMEM184A	ENST00000319018.12	n.*594_*599dupGGCGGC		non_coding_transcript_exon_variant	Exon 8 of 8	5		ENSP00000326348.7
TMEM184A	ENST00000468535.5	n.2049_2054dupGGCGGC		non_coding_transcript_exon_variant	Exon 6 of 6	2
TMEM184A	ENST00000319018.12	n.*594_*599dupGGCGGC		3_prime_UTR_variant	Exon 8 of 8	5		ENSP00000326348.7

Frequencies

GnomAD3 genomes AF: 0.0000198 AC: 3 AN: 151280 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000657

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000296

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000415 AC: 6 AN: 1445624 Hom.: 0 Cov.: 54 AF XY: 0.00 AC XY: 0 AN XY: 719172

Gnomad4 AFR exome AF: 0.0000301

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000253

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000361

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000198 AC: 3 AN: 151280 Hom.: 0 Cov.: 0 AF XY: 0.0000135 AC XY: 1 AN XY: 73840

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000657

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000296

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112463195; hg19: chr7-1586653;