chrX-120875109-C-G

Variant names:

• chrX-120875109-C-G
• rs752483454
• NM_001145718.3:c.562G>C

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_001145718.3(CT47B1):​c.562G>C​(p.Gly188Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000414 in 1,208,636 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G188S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00023 (0 hom., 9 hem., cov: 22)
  • Exomes 𝑓: 0.000022 (0 hom. 8 hem.)
• Consequence: CT47B1 NM_001145718.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.761
• Publications: 2 publications found

Genes affected

CT47B1 (HGNC:33293): (cancer/testis antigen family 47 member B1)

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.07889384).
• BS2: High Hemizygotes in GnomAd4 at 9 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145718.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CT47B1	NM_001145718.3	MANE Select	c.562G>C	p.Gly188Arg	missense	Exon 1 of 3	NP_001139190.1	P0C2W7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CT47B1	ENST00000371311.5	TSL:5 MANE Select	c.562G>C	p.Gly188Arg	missense	Exon 1 of 3	ENSP00000360360.3	P0C2W7

Frequencies

GnomAD3 genomes AF: 0.000231 AC: 26 AN: 112499 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.000840

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000607 AC: 11 AN: 181292 AF XY: 0.0000298

Gnomad AFR exome AF: 0.000631

Gnomad AMR exome AF: 0.0000366

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000124

Gnomad OTH exome AF: 0.000223

GnomAD4 exome AF: 0.0000219 AC: 24 AN: 1096137 Hom.: 0 Cov.: 31 AF XY: 0.0000221 AC XY: 8 AN XY: 362229

African (AFR) AF: 0.000683 AC: 18 AN: 26368

American (AMR) AF: 0.0000569 AC: 2 AN: 35169

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19346

East Asian (EAS) AF: 0.00 AC: 0 AN: 30188

South Asian (SAS) AF: 0.0000185 AC: 1 AN: 54045

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40315

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3421

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 841314

Other (OTH) AF: 0.0000653 AC: 3 AN: 45971

GnomAD4 genome AF: 0.000231 AC: 26 AN: 112499 Hom.: 0 Cov.: 22 AF XY: 0.000260 AC XY: 9 AN XY: 34667

African (AFR) AF: 0.000840 AC: 26 AN: 30968

American (AMR) AF: 0.00 AC: 0 AN: 10757

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2650

East Asian (EAS) AF: 0.00 AC: 0 AN: 3550

South Asian (SAS) AF: 0.00 AC: 0 AN: 2766

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6223

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 238

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53146

Other (OTH) AF: 0.00 AC: 0 AN: 1518

Alfa AF: 0.0000434 Hom.: 0

Bravo AF: 0.000249

ExAC AF: 0.0000746 AC: 9

EpiCase AF: 0.0000546

EpiControl AF: 0.0000594

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.45
BayesDel_addAF	Benign	-0.51	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	8.4
DANN	Uncertain	0.99
DEOGEN2	Benign	0.13	T
FATHMM_MKL	Benign	0.022	N
LIST_S2	Benign	0.63	T
M_CAP	Benign	0.0023	T
MetaRNN	Benign	0.079	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.2	M
PhyloP100		-0.76
PrimateAI	Benign	0.43	T
PROVEAN	Uncertain	-3.3	D
REVEL	Benign	0.034
Sift	Uncertain	0.0040	D
Sift4G	Benign	0.18	T
Polyphen		1.0	D
Vest4		0.023
MVP		0.085
MPC		0.024
ClinPred		0.24	T
GERP RS		2.0
Varity_R		0.22
gMVP		0.018
Mutation Taster		=98/2	polymorphism

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: rs752483454; hg19: chrX-120008963; COSMIC: COSV64890371; COSMIC: COSV64890371;