X-120873930-A-T

Variant names:

• chrX-120873930-A-T
• rs767296022
• NM_001145718.3:c.866T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001145718.3(CT47B1):​c.866T>A​(p.Val289Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000926 in 1,079,573 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V289A) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 12)
  • Exomes 𝑓: 9.3e-7 (0 hom. 1 hem.)
• Consequence: CT47B1 NM_001145718.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0506486).

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.866T>A	p.Val289Glu	missense	Exon 2 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.866T>A	p.Val289Glu	missense	Exon 2 of 3	ENSP00000360360.3	P0C2W7

Frequencies

GnomAD3 genomes Cov.: 12

GnomAD4 exome AF: 9.26e-7 AC: 1 AN: 1079573 Hom.: 0 Cov.: 31 AF XY: 0.00000282 AC XY: 1 AN XY: 354447

African (AFR) AF: 0.00 AC: 0 AN: 26246

American (AMR) AF: 0.00 AC: 0 AN: 35064

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18991

East Asian (EAS) AF: 0.00 AC: 0 AN: 29965

South Asian (SAS) AF: 0.00 AC: 0 AN: 53951

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29195

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3238

European-Non Finnish (NFE) AF: 0.00000119 AC: 1 AN: 837367

Other (OTH) AF: 0.00 AC: 0 AN: 45556

GnomAD4 genome Cov.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Benign	-0.45	T
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.016
DANN	Benign	0.49
DEOGEN2	Benign	0.0035	T
FATHMM_MKL	Benign	0.00033	N
LIST_S2	Benign	0.21	T
M_CAP	Benign	0.0084	T
MetaRNN	Benign	0.051	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		-1.8
PrimateAI	Benign	0.24	T
PROVEAN	Benign	0.38	N
REVEL	Benign	0.067
Sift	Benign	0.27	T
Sift4G	Benign	0.068	T
Polyphen		0.0	B
Vest4		0.11
MutPred		0.19		Loss of MoRF binding (P = 0.0125)
MVP		0.23
MPC		0.0045
ClinPred		0.070	T
GERP RS		-2.3
Varity_R		0.12
gMVP		0.0013
Mutation Taster		=100/0	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: rs767296022; hg19: chrX-120007784;