chr7-1556560-A-G

Variant names:

• chr7-1556560-A-G
• rs7811444
• ENST00000431208.1:c.1-1076T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

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.

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	c.1-1076T>C		intron_variant	Intron 1 of 3	4		ENSP00000403499.1
TMEM184A	ENST00000421923.5	n.1-1076T>C		intron_variant	Intron 1 of 5	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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.400 AC: 8 AN: 20

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.304 AC: 17 AN: 56

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.308 AC: 46862 AN: 152076 Hom.: 8373 Cov.: 33 AF XY: 0.301 AC XY: 22352 AN XY: 74340

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: 60 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16995 AN: 67948

Other (OTH) AF: 0.301 AC: 635 AN: 2108

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.66
PromoterAI		-0.022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7811444; hg19: chr7-1596196;