chr3-169926668-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.406C>T​(p.Pro136Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SAMD7
NM_001304366.2 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.21
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]

Genome browser will be placed here

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=0.24469459).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SAMD7NM_001304366.2 linkc.406C>T p.Pro136Ser missense_variant Exon 6 of 9 ENST00000335556.7 NP_001291295.1 Q7Z3H4
SAMD7NM_182610.4 linkc.406C>T p.Pro136Ser missense_variant Exon 6 of 9 NP_872416.1 Q7Z3H4
SAMD7NR_130713.2 linkn.885C>T non_coding_transcript_exon_variant Exon 7 of 10

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SAMD7ENST00000335556.7 linkc.406C>T p.Pro136Ser missense_variant Exon 6 of 9 1 NM_001304366.2 ENSP00000334668.3 Q7Z3H4
SAMD7ENST00000428432.6 linkc.406C>T p.Pro136Ser missense_variant Exon 6 of 9 1 ENSP00000391299.2 Q7Z3H4
SAMD7ENST00000487910.1 linkn.*222C>T non_coding_transcript_exon_variant Exon 6 of 9 1 ENSP00000420460.1 F8WDF1
SAMD7ENST00000487910.1 linkn.*222C>T 3_prime_UTR_variant Exon 6 of 9 1 ENSP00000420460.1 F8WDF1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251356
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135892
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461860
Hom.:
0
Cov.:
32
AF XY:
0.00000275
AC XY:
2
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Oct 21, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.406C>T (p.P136S) alteration is located in exon 6 (coding exon 4) of the SAMD7 gene. This alteration results from a C to T substitution at nucleotide position 406, causing the proline (P) at amino acid position 136 to be replaced by a serine (S). 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
0.087
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
11
DANN
Uncertain
1.0
DEOGEN2
Benign
0.025
T;T
Eigen
Benign
-0.069
Eigen_PC
Benign
-0.17
FATHMM_MKL
Benign
0.60
D
LIST_S2
Benign
0.50
.;T
M_CAP
Benign
0.035
D
MetaRNN
Benign
0.24
T;T
MetaSVM
Benign
-0.54
T
MutationAssessor
Uncertain
2.7
M;M
PrimateAI
Benign
0.28
T
PROVEAN
Uncertain
-2.8
D;D
REVEL
Benign
0.19
Sift
Benign
0.031
D;D
Sift4G
Uncertain
0.046
D;D
Polyphen
0.95
P;P
Vest4
0.13
MutPred
0.36
Gain of catalytic residue at P136 (P = 0.0245);Gain of catalytic residue at P136 (P = 0.0245);
MVP
0.76
MPC
0.17
ClinPred
0.87
D
GERP RS
5.3
Varity_R
0.13
gMVP
0.48

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1200391348; hg19: chr3-169644456; API