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GeneBe

7-127704919-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_014390.4(SND1):c.921C>T(p.Gly307=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00157 in 1,613,944 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0080 ( 17 hom., cov: 33)
Exomes 𝑓: 0.00090 ( 16 hom. )

Consequence

SND1
NM_014390.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.06
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 -15 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=-0.57).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-127704919-C-T is Benign according to our data. Variant chr7-127704919-C-T is described in ClinVar as [Benign]. Clinvar id is 787864.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=-5.06 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00796 (1211/152192) while in subpopulation AFR AF= 0.0271 (1123/41510). AF 95% confidence interval is 0.0257. There are 17 homozygotes in gnomad4. There are 571 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
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 1204 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SND1NM_014390.4 linkuse as main transcriptc.921C>T p.Gly307= synonymous_variant 8/24 ENST00000354725.8
SND1XM_017011987.3 linkuse as main transcriptc.921C>T p.Gly307= synonymous_variant 8/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SND1ENST00000354725.8 linkuse as main transcriptc.921C>T p.Gly307= synonymous_variant 8/241 NM_014390.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00792
AC:
1204
AN:
152074
Hom.:
17
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0270
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00374
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000220
Gnomad OTH
AF:
0.00574
GnomAD3 exomes
AF:
0.00214
AC:
538
AN:
251158
Hom.:
10
AF XY:
0.00152
AC XY:
206
AN XY:
135724
show subpopulations
Gnomad AFR exome
AF:
0.0273
Gnomad AMR exome
AF:
0.00182
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000211
Gnomad OTH exome
AF:
0.000816
GnomAD4 exome
AF:
0.000900
AC:
1315
AN:
1461752
Hom.:
16
Cov.:
30
AF XY:
0.000763
AC XY:
555
AN XY:
727184
show subpopulations
Gnomad4 AFR exome
AF:
0.0265
Gnomad4 AMR exome
AF:
0.00224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000165
Gnomad4 OTH exome
AF:
0.00200
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00796
AC:
1211
AN:
152192
Hom.:
17
Cov.:
33
AF XY:
0.00767
AC XY:
571
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.0271
Gnomad4 AMR
AF:
0.00373
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.00568
Alfa
AF:
0.00362
Hom.:
1
Bravo
AF:
0.00929
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.000600
EpiControl
AF:
0.000119

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
Cadd
Benign
0.68
Dann
Benign
0.63
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs115701447; hg19: chr7-127344973; API