11-106009930-C-G

Variant names:

• chr11-106009930-C-G
• NM_032424.3:c.643G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_032424.3(MSANTD4):​c.643G>C​(p.Glu215Gln) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MSANTD4 NM_032424.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.94
• Publications: 0 publications found

Genes affected

MSANTD4 (HGNC:29383): (Myb/SANT DNA binding domain containing 4 with coiled-coils) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032424.3. 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
	MSANTD4	NM_032424.3	MANE Select	c.643G>C	p.Glu215Gln	missense	Exon 3 of 3	NP_115800.1	Q8NCY6
	MSANTD4	NM_001318747.1		c.643G>C	p.Glu215Gln	missense	Exon 3 of 3	NP_001305676.1	Q8NCY6
	MSANTD4	NM_001318748.1		c.643G>C	p.Glu215Gln	missense	Exon 3 of 3	NP_001305677.1	Q8NCY6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSANTD4	ENST00000301919.9	TSL:1 MANE Select	c.643G>C	p.Glu215Gln	missense	Exon 3 of 3	ENSP00000304713.4	Q8NCY6
	MSANTD4	ENST00000874422.1		c.643G>C	p.Glu215Gln	missense	Exon 4 of 4	ENSP00000544481.1
	MSANTD4	ENST00000874423.1		c.643G>C	p.Glu215Gln	missense	Exon 4 of 4	ENSP00000544482.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

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	0.49
BayesDel_addAF	Uncertain	0.035	T
BayesDel_noAF	Benign	-0.19
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Benign	0.10	T
Eigen	Uncertain	0.50
Eigen_PC	Uncertain	0.48
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.91	D
M_CAP	Benign	0.018	T
MetaRNN	Uncertain	0.49	T
MetaSVM	Benign	-0.53	T
MutationAssessor	Benign	1.1	L
PhyloP100		6.9
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.27
Sift	Uncertain	0.022	D
Sift4G	Uncertain	0.014	D
Polyphen		0.98	D
Vest4		0.63
MutPred		0.11		Gain of MoRF binding (P = 0.0226)
MVP		0.33
MPC		1.0
ClinPred		0.93	D
GERP RS		5.8
Varity_R		0.22
gMVP		0.45
Mutation Taster		=53/47	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

hg19: chr11-105880657;