3-169919527-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001304366.2(SAMD7):​c.29C>T​(p.Thr10Ile) 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

SAMD7
NM_001304366.2 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.44
Variant links:
Genes affected
SAMD7 (HGNC:25394): (sterile alpha motif domain containing 7) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

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=0.09747282).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SAMD7NM_001304366.2 linkc.29C>T p.Thr10Ile missense_variant Exon 3 of 9 ENST00000335556.7 NP_001291295.1 Q7Z3H4
SAMD7NM_182610.4 linkc.29C>T p.Thr10Ile missense_variant Exon 3 of 9 NP_872416.1 Q7Z3H4
SAMD7NR_130713.2 linkn.395C>T non_coding_transcript_exon_variant Exon 3 of 10

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SAMD7ENST00000335556.7 linkc.29C>T p.Thr10Ile missense_variant Exon 3 of 9 1 NM_001304366.2 ENSP00000334668.3 Q7Z3H4
SAMD7ENST00000428432.6 linkc.29C>T p.Thr10Ile missense_variant Exon 3 of 9 1 ENSP00000391299.2 Q7Z3H4
SAMD7ENST00000487910.1 linkn.29C>T non_coding_transcript_exon_variant Exon 2 of 9 1 ENSP00000420460.1 F8WDF1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
May 16, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.29C>T (p.T10I) alteration is located in exon 3 (coding exon 1) of the SAMD7 gene. This alteration results from a C to T substitution at nucleotide position 29, causing the threonine (T) at amino acid position 10 to be replaced by an isoleucine (I). 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
0.12
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
17
DANN
Benign
0.97
DEOGEN2
Benign
0.0041
T;T
Eigen
Benign
-0.79
Eigen_PC
Benign
-0.77
FATHMM_MKL
Benign
0.19
N
LIST_S2
Benign
0.42
.;T
M_CAP
Benign
0.0092
T
MetaRNN
Benign
0.097
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.34
N;N
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-1.6
N;N
REVEL
Benign
0.059
Sift
Benign
0.061
T;T
Sift4G
Benign
0.12
T;T
Polyphen
0.0050
B;B
Vest4
0.28
MutPred
0.13
Loss of glycosylation at T10 (P = 0.0217);Loss of glycosylation at T10 (P = 0.0217);
MVP
0.48
MPC
0.15
ClinPred
0.11
T
GERP RS
3.3
Varity_R
0.069
gMVP
0.19

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: chr3-169637315; API