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GeneBe

7-127652388-G-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_014390.4(SND1):c.15G>C(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000657 in 1,598,812 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00075 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00065 ( 5 hom. )

Consequence

SND1
NM_014390.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.16
Variant links:
Genes affected
SND1 (HGNC:30646): (staphylococcal nuclease and tudor domain containing 1) This gene encodes a transcriptional co-activator that interacts with the acidic domain of Epstein-Barr virus nuclear antigen 2 (EBNA 2), a transcriptional activator that is required for B-lymphocyte transformation. Other transcription factors that interact with this protein are signal transducers and activators of transcription, STATs. This protein is also thought to be essential for normal cell growth. A similar protein in mammals and other organisms is a component of the RNA-induced silencing complex (RISC). [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-127652388-G-C is Benign according to our data. Variant chr7-127652388-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 726681.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.16 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 115 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SND1NM_014390.4 linkuse as main transcriptc.15G>C p.Ala5= synonymous_variant 1/24 ENST00000354725.8
SND1XM_017011987.3 linkuse as main transcriptc.15G>C p.Ala5= synonymous_variant 1/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SND1ENST00000354725.8 linkuse as main transcriptc.15G>C p.Ala5= synonymous_variant 1/241 NM_014390.4 P1
SND1ENST00000463020.1 linkuse as main transcriptn.195G>C non_coding_transcript_exon_variant 1/22

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000756
AC:
115
AN:
152210
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00177
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000955
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000911
AC:
200
AN:
219532
Hom.:
2
AF XY:
0.00104
AC XY:
124
AN XY:
118786
show subpopulations
Gnomad AFR exome
AF:
0.0000763
Gnomad AMR exome
AF:
0.000796
Gnomad ASJ exome
AF:
0.00181
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00157
Gnomad FIN exome
AF:
0.0000555
Gnomad NFE exome
AF:
0.00105
Gnomad OTH exome
AF:
0.00185
GnomAD4 exome
AF:
0.000646
AC:
935
AN:
1446484
Hom.:
5
Cov.:
30
AF XY:
0.000709
AC XY:
509
AN XY:
717872
show subpopulations
Gnomad4 AFR exome
AF:
0.0000300
Gnomad4 AMR exome
AF:
0.000902
Gnomad4 ASJ exome
AF:
0.00187
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00116
Gnomad4 FIN exome
AF:
0.0000385
Gnomad4 NFE exome
AF:
0.000591
Gnomad4 OTH exome
AF:
0.00105
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000755
AC:
115
AN:
152328
Hom.:
1
Cov.:
33
AF XY:
0.000685
AC XY:
51
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.00176
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.000941
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000983
Hom.:
2
Bravo
AF:
0.000695
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeOct 23, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.32
Cadd
Benign
14
Dann
Benign
0.87

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: rs145576520; hg19: chr7-127292442; COSMIC: COSV61249407; COSMIC: COSV61249407; API