dbSNP rs551818024: MSANTD1:p.Ala13Gly (chr4-3249260-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001042690.2(MSANTD1):c.38C>G(p.Ala13Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000151 in 1,328,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. A13V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 34)

Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

MSANTD1
NM_001042690.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.80

Publications

0 publications found

Variant links:

Genes affected

MSANTD1 (HGNC:33741): (Myb/SANT DNA binding domain containing 1) Predicted to be involved in positive regulation of transcription, DNA-templated. Predicted to be active in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

MSANTD1 links:

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ACMG classification

Classification was made for transcript

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=0.059182525).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSANTD1	NM_001042690.2 link	c.38C>G	p.Ala13Gly	missense_variant	Exon 1 of 3	ENST00000438480.7	NP_001036155.1	Q6ZTZ1
MSANTD1	XM_011513467.4 link	c.38C>G	p.Ala13Gly	missense_variant	Exon 1 of 2		XP_011511769.1
MSANTD1	NM_001330620.2 link	c.17-18C>G		intron_variant	Intron 3 of 5		NP_001317549.1	D6R9L8
MSANTD1	XM_047415655.1 link	c.17-18C>G		intron_variant	Intron 1 of 2		XP_047271611.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
MSANTD1	ENST00000438480.7 link	c.38C>G	p.Ala13Gly	missense_variant	Exon 1 of 3	5	NM_001042690.2	ENSP00000411584.2	Q6ZTZ1
MSANTD1	ENST00000507492.5 link	c.17-18C>G		intron_variant	Intron 3 of 5	1		ENSP00000423547.1	D6R9L8
MSANTD1	ENST00000510580.1 link	c.38C>G	p.Ala13Gly	missense_variant	Exon 1 of 4	5		ENSP00000420966.1	D6RDG6
MSANTD1	ENST00000505599.5 link	n.38C>G		non_coding_transcript_exon_variant	Exon 1 of 6	2		ENSP00000425405.1	D6RD98

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000151

AC:

AN:

1328174

Hom.:

Cov.:

AF XY:

0.00000154

AC XY:

AN XY:

647622

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29632

American (AMR)

AF:

0.00

AC:

AN:

27716

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21064

East Asian (EAS)

AF:

0.0000573

AC:

AN:

34914

South Asian (SAS)

AF:

0.00

AC:

AN:

70052

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40318

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4746

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1044870

Other (OTH)

AF:

0.00

AC:

AN:

54862

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.60

CADD

Benign

8.6

(source)

DANN

Benign

0.83

DEOGEN2

Benign

0.0026

T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.27

LIST_S2

Benign

0.34

T;T

M_CAP

Benign

0.013

MetaRNN

Benign

0.059

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.0

L;.

PhyloP100

1.8

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-0.94

N;N

REVEL

Benign

0.020

Sift

Benign

0.034

D;D

Sift4G

Benign

0.27

T;T

Polyphen

0.093

B;.

Vest4

0.082

MutPred

0.13

Gain of relative solvent accessibility (P = 0.0082);Gain of relative solvent accessibility (P = 0.0082);

MVP

0.014

MPC

0.32

ClinPred

0.10

GERP RS

1.1

PromoterAI

-0.042

Neutral

(source)

Varity_R

0.057

gMVP

0.31

Mutation Taster

=98/2

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over