2-238848306-C-G

Position:

• chr2-238848306-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1 PM2 BP4

The NM_001271893.4(TWIST2):​c.91C>G​(p.Arg31Gly) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TWIST2 NM_001271893.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34

Genes affected

TWIST2 (HGNC:20670): (twist family bHLH transcription factor 2) The protein encoded by this gene is a basic helix-loop-helix type transcription factor and shares similarity with Twist. This protein may inhibit osteoblast maturation and maintain cells in a preosteoblast phenotype during osteoblast development. This gene may be upregulated in certain cancers. Mutations in this gene cause focal facial dermal dysplasia 3, Setleis type. Two transcript variants encoding the same protein have been found. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM1: In a chain Twist-related protein 2 (size 159) in uniprot entity TWST2_HUMAN there are 5 pathogenic changes around while only 1 benign (83%) in NM_001271893.4
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.35597008).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TWIST2	NM_001271893.4	c.91C>G	p.Arg31Gly	missense_variant	1/2	ENST00000612363.2
TWIST2	NM_057179.3	c.91C>G	p.Arg31Gly	missense_variant	1/2
TWIST2	XR_007069137.1	n.222C>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TWIST2	ENST00000612363.2	c.91C>G	p.Arg31Gly	missense_variant	1/2	1	NM_001271893.4	P1
TWIST2	ENST00000448943.2	c.91C>G	p.Arg31Gly	missense_variant	1/2	1		P1
TWIST2	ENST00000710607.1	c.91C>G	p.Arg31Gly	missense_variant	1/2			P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.44
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.0
CADD	Uncertain	23
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.46	T;T
Eigen	Uncertain	0.20
Eigen_PC	Benign	0.20
FATHMM_MKL	Benign	0.73	D
M_CAP	Pathogenic	0.49	D
MetaRNN	Benign	0.36	T;T
MetaSVM	Pathogenic	0.84	D
MutationAssessor	Benign	1.9	M;M
MutationTaster	Benign	0.98	D
PrimateAI	Pathogenic	0.86	D
PROVEAN	Uncertain	-2.6	D;.
REVEL	Uncertain	0.60
Sift	Benign	0.091	T;.
Sift4G	Uncertain	0.0070	D;D
Polyphen		0.70	P;P
Vest4		0.20
MutPred		0.24		Loss of MoRF binding (P = 0.0736);Loss of MoRF binding (P = 0.0736);
MVP		0.99
MPC		2.0
ClinPred		0.93	D
GERP RS		2.8
Varity_R		0.22
gMVP		0.90

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: chr2-239756947;