NM_031442.4:c.*150C>T

Variant names:

• chrX-34630163-G-A
• rs10522027
• NM_031442.4:c.*150C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031442.4(TMEM47):​c.*150C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 525,871 control chromosomes in the GnomAD database, including 6,739 homozygotes. There are 24,702 hemizygotes in GnomAD. 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 0.14 (1077 hom., 5003 hem., cov: 23)
  • Exomes 𝑓: 0.17 (5662 hom. 19699 hem.)
• Consequence: TMEM47 NM_031442.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 4 publications found

Genes affected

TMEM47 (HGNC:18515): (transmembrane protein 47) This gene encodes a member of the PMP22/EMP/claudin protein family. The encoded protein is localized to the ER and the plasma membrane. In dogs, transcripts of this gene exist at high levels in the brain. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM47	NM_031442.4	c.*150C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000275954.4	NP_113630.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM47	ENST00000275954.4	c.*150C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_031442.4	ENSP00000275954.3

Frequencies

GnomAD3 genomes AF: 0.143 AC: 16025 AN: 112016 Hom.: 1076 Cov.: 23

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.188

GnomAD4 exome AF: 0.174 AC: 72060 AN: 413802 Hom.: 5662 Cov.: 6 AF XY: 0.187 AC XY: 19699 AN XY: 105282

African (AFR) AF: 0.0507 AC: 610 AN: 12020

American (AMR) AF: 0.324 AC: 4124 AN: 12746

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 1856 AN: 9332

East Asian (EAS) AF: 0.453 AC: 10963 AN: 24208

South Asian (SAS) AF: 0.295 AC: 4422 AN: 14988

European-Finnish (FIN) AF: 0.126 AC: 3845 AN: 30461

Middle Eastern (MID) AF: 0.163 AC: 238 AN: 1463

European-Non Finnish (NFE) AF: 0.147 AC: 42182 AN: 287239

Other (OTH) AF: 0.179 AC: 3820 AN: 21345

GnomAD4 genome AF: 0.143 AC: 16026 AN: 112069 Hom.: 1077 Cov.: 23 AF XY: 0.146 AC XY: 5003 AN XY: 34261

African (AFR) AF: 0.0533 AC: 1649 AN: 30961

American (AMR) AF: 0.246 AC: 2594 AN: 10531

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 523 AN: 2646

East Asian (EAS) AF: 0.476 AC: 1668 AN: 3504

South Asian (SAS) AF: 0.299 AC: 813 AN: 2721

European-Finnish (FIN) AF: 0.121 AC: 738 AN: 6084

Middle Eastern (MID) AF: 0.135 AC: 29 AN: 215

European-Non Finnish (NFE) AF: 0.143 AC: 7603 AN: 53188

Other (OTH) AF: 0.188 AC: 289 AN: 1539

Alfa AF: 0.149 Hom.: 11012

Bravo AF: 0.155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10522027; hg19: chrX-34648280; COSMIC: COSV52068569;