15-74410879-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_003612.5(SEMA7A):c.1746C>T(p.Asn582=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,614,194 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 Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000043 ( 0 hom. )
Consequence
SEMA7A
NM_003612.5 synonymous
NM_003612.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
Genes affected
SEMA7A (HGNC:10741): (semaphorin 7A (JohnMiltonHagen blood group)) This gene encodes a member of the semaphorin family of proteins. The encoded preproprotein is proteolytically processed to generate the mature glycosylphosphatidylinositol (GPI)-anchored membrane glycoprotein. The encoded protein is found on activated lymphocytes and erythrocytes and may be involved in immunomodulatory and neuronal processes. The encoded protein carries the John Milton Hagen (JMH) blood group antigens. Mutations in this gene may be associated with reduced bone mineral density (BMD). Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
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Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
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Variant 15-74410879-G-A is Benign according to our data. Variant chr15-74410879-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2681535.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
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Synonymous conserved (PhyloP=-1.21 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA7A | NM_003612.5 | c.1746C>T | p.Asn582= | synonymous_variant | 14/14 | ENST00000261918.9 | |
SEMA7A | NM_001146029.3 | c.1704C>T | p.Asn568= | synonymous_variant | 13/13 | ||
SEMA7A | NM_001146030.3 | c.1251C>T | p.Asn417= | synonymous_variant | 14/14 | ||
SEMA7A | XM_047433177.1 | c.1623C>T | p.Asn541= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA7A | ENST00000261918.9 | c.1746C>T | p.Asn582= | synonymous_variant | 14/14 | 1 | NM_003612.5 | P1 | |
SEMA7A | ENST00000543145.6 | c.1704C>T | p.Asn568= | synonymous_variant | 13/13 | 2 | |||
SEMA7A | ENST00000542748.6 | c.1251C>T | p.Asn417= | synonymous_variant | 14/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152206Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251448Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135898
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GnomAD4 exome AF: 0.0000431 AC: 63AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000564 AC XY: 41AN XY: 727236
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GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
EBV-positive nodal T- and NK-cell lymphoma Benign:1
Likely benign, no assertion criteria provided | research | Department of Clinical Pathology, School of Medicine, Fujita Health University | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at