X-72302842-C-T

Position:

• chrX-72302842-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP6

The NM_001144887.2(CITED1):​c.28G>A​(p.Asp10Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: not found (cov: 25)
• Consequence: CITED1 NM_001144887.2 missense
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 2.94

Genes affected

CITED1 (HGNC:1986): (Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1) This gene encodes a member of the CREB-binding protein/p300-interacting transactivator with Asp/Glu-rich C-terminal domain (CITED) family of proteins. The encoded protein, also known as melanocyte-specific gene 1, may function as a transcriptional coactivator and may play a role in pigmentation of melanocytes. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]

ENSG00000285547 (HGNC:):

PIN4 (HGNC:8992): (peptidylprolyl cis/trans isomerase, NIMA-interacting 4) This gene encodes a member of the parvulin subfamily of the peptidyl-prolyl cis/trans isomerase protein family. The encoded protein catalyzes the isomerization of peptidylprolyl bonds, and may play a role in the cell cycle, chromatin remodeling, and/or ribosome biogenesis. The encoded protein may play an additional role in the mitochondria. [provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22656855).
• BP6: Variant X-72302842-C-T is Benign according to our data. Variant chrX-72302842-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2681726.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CITED1	NM_001144887.2	c.28G>A	p.Asp10Asn	missense_variant	2/3	ENST00000651998.1	NP_001138359.1
CITED1	NM_001144885.2	c.106G>A	p.Asp36Asn	missense_variant	3/4		NP_001138357.1
CITED1	NM_001144886.2	c.28G>A	p.Asp10Asn	missense_variant	2/3		NP_001138358.1
CITED1	NM_004143.4	c.28G>A	p.Asp10Asn	missense_variant	2/3		NP_004134.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CITED1	ENST00000651998.1	c.28G>A	p.Asp10Asn	missense_variant	2/3		NM_001144887.2	ENSP00000499148.1
ENSG00000285547	ENST00000648922.1	c.1204G>A	p.Asp402Asn	missense_variant	11/12			ENSP00000497072.1

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 25

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.11	.;.;T;T;T;T;T;.;T;.
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Uncertain	0.88	.;D;D;.;.;D;D;D;D;D
M_CAP	Benign	0.028	D
MetaRNN	Benign	0.23	T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.35	T
MutationAssessor	Benign	1.1	.;.;L;L;L;.;.;.;.;.
MutationTaster	Benign	0.59	N;N;N;N;N
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-0.40	N;N;N;N;N;D;D;D;D;.
REVEL	Benign	0.13
Sift	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;.
Sift4G	Benign	0.17	T;T;T;T;T;.;.;.;D;.
Polyphen		1.0	D;D;D;D;D;.;.;.;.;.
Vest4		0.42
MutPred		0.21		.;.;Gain of MoRF binding (P = 0.0186);Gain of MoRF binding (P = 0.0186);Gain of MoRF binding (P = 0.0186);Gain of MoRF binding (P = 0.0186);.;.;.;.;
MVP		0.83
MPC		0.55
ClinPred		0.80	D
GERP RS		4.1
Varity_R		0.17
gMVP		0.38

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-71522692;