7-1556560-A-G

Position:

• chr7-1556560-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

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]

(HGNC:):

ACMG classification

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/exons	MANE	Protein	UniProt
		n.1556560A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM184A	ENST00000431208.1	c.1-1076T>C		intron_variant		4		ENSP00000403499.1
TMEM184A	ENST00000421923.5	n.1-1076T>C		intron_variant		5		ENSP00000413955.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46779 AN: 151958 Hom.: 8344 Cov.: 33

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: 31 AN: 94 Hom.: 6 AF XY: 0.328 AC XY: 21 AN XY: 64

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.: 33 AF XY: 0.301 AC XY: 22352 AN XY: 74340

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

Other links and lift over

dbSNP: rs7811444; hg19: chr7-1596196;