chr6-70755016-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001044305.3(SMAP1):c.289C>T(p.Leu97Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000891 in 1,458,394 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
SMAP1
NM_001044305.3 missense
NM_001044305.3 missense
Scores
1
6
12
Clinical Significance
Conservation
PhyloP100: 3.06
Genes affected
SMAP1 (HGNC:19651): (small ArfGAP 1) The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.33883902).
BS2
High AC in GnomAdExome4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMAP1 | NM_001044305.3 | c.289C>T | p.Leu97Phe | missense_variant | 3/11 | ENST00000370455.8 | NP_001037770.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMAP1 | ENST00000370455.8 | c.289C>T | p.Leu97Phe | missense_variant | 3/11 | 1 | NM_001044305.3 | ENSP00000359484 | P3 | |
SMAP1 | ENST00000619054.4 | c.259C>T | p.Leu87Phe | missense_variant | 3/11 | 1 | ENSP00000484538 | |||
SMAP1 | ENST00000316999.9 | c.289C>T | p.Leu97Phe | missense_variant | 3/10 | 1 | ENSP00000313382 | A1 | ||
SMAP1 | ENST00000370452.7 | c.289C>T | p.Leu97Phe | missense_variant | 3/11 | 2 | ENSP00000359481 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458394Hom.: 0 Cov.: 30 AF XY: 0.00000827 AC XY: 6AN XY: 725514
GnomAD4 exome
AF:
AC:
13
AN:
1458394
Hom.:
Cov.:
30
AF XY:
AC XY:
6
AN XY:
725514
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 29, 2024 | The c.289C>T (p.L97F) alteration is located in exon 3 (coding exon 3) of the SMAP1 gene. This alteration results from a C to T substitution at nucleotide position 289, causing the leucine (L) at amino acid position 97 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;.
REVEL
Benign
Sift
Benign
T;T;T;.
Sift4G
Uncertain
T;T;T;D
Polyphen
B;B;D;.
Vest4
MutPred
Gain of helix (P = 0.132);Gain of helix (P = 0.132);Gain of helix (P = 0.132);.;
MVP
MPC
0.60
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.