11-124800178-A-C

Position:

• chr11-124800178-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001308027.2(MSANTD2):​c.203T>G​(p.Leu68Arg) 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: MSANTD2 NM_001308027.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.659

Genes affected

MSANTD2 (HGNC:26266): (Myb/SANT DNA binding domain containing 2)

MSANTD2 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17135862).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSANTD2	NM_001308027.2	c.203T>G	p.Leu68Arg	missense_variant	1/4	ENST00000374979.8	NP_001294956.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSANTD2	ENST00000374979.8	c.203T>G	p.Leu68Arg	missense_variant	1/4	1	NM_001308027.2	ENSP00000364118.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 04, 2021

The c.203T>G (p.L68R) alteration is located in exon 1 (coding exon 1) of the MSANTD2 gene. This alteration results from a T to G substitution at nucleotide position 203, causing the leucine (L) at amino acid position 68 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Uncertain	0.080	D
BayesDel_noAF	Benign	-0.12
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.021	.;T;.
Eigen	Benign	0.074
Eigen_PC	Benign	0.16
FATHMM_MKL	Benign	0.53	D
LIST_S2	Benign	0.73	T;T;T
M_CAP	Uncertain	0.12	D
MetaRNN	Benign	0.17	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N;N;.
PrimateAI	Pathogenic	0.94	D
PROVEAN	Benign	-0.79	N;N;N
REVEL	Benign	0.20
Sift	Benign	0.055	T;D;T
Sift4G	Benign	0.35	T;T;T
Polyphen		0.87	P;P;.
Vest4		0.31
MutPred		0.31		Gain of methylation at L68 (P = 0.0023);Gain of methylation at L68 (P = 0.0023);Gain of methylation at L68 (P = 0.0023);
MVP		0.068
MPC		1.1
ClinPred		0.37	T
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		3.2
Varity_R		0.44
gMVP		0.33

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: chr11-124670074;