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GeneBe

7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PM1PM4BP6_ModerateBS1BS2

The NM_014390.4(SND1):c.14_34dup(p.Ala5_Ser11dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,596,444 control chromosomes in the GnomAD database, including 162 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0078 ( 19 hom., cov: 33)
Exomes 𝑓: 0.011 ( 143 hom. )

Consequence

SND1
NM_014390.4 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.70
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PM1
?
    PM1 - Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
In a modified_residue N-acetylalanine (size 0) in uniprot entity SND1_HUMAN
PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Nonframeshift variant in NON repetitive region in NM_014390.4.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC is Benign according to our data. Variant chr7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC is described in ClinVar as [Benign]. Clinvar id is 718333.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00775 (1181/152306) while in subpopulation SAS AF= 0.0423 (204/4824). AF 95% confidence interval is 0.0375. There are 19 homozygotes in gnomad4. There are 591 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 1181 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SND1NM_014390.4 linkuse as main transcriptc.14_34dup p.Ala5_Ser11dup inframe_insertion 1/24 ENST00000354725.8
SND1XM_017011987.3 linkuse as main transcriptc.14_34dup p.Ala5_Ser11dup inframe_insertion 1/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SND1ENST00000354725.8 linkuse as main transcriptc.14_34dup p.Ala5_Ser11dup inframe_insertion 1/241 NM_014390.4 P1
SND1ENST00000463020.1 linkuse as main transcriptn.194_214dup non_coding_transcript_exon_variant 1/22

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00776
AC:
1181
AN:
152188
Hom.:
19
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00169
Gnomad AMI
AF:
0.0208
Gnomad AMR
AF:
0.00419
Gnomad ASJ
AF:
0.00519
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0420
Gnomad FIN
AF:
0.0110
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00980
Gnomad OTH
AF:
0.00860
GnomAD3 exomes
AF:
0.00789
AC:
1706
AN:
216140
Hom.:
25
AF XY:
0.00900
AC XY:
1048
AN XY:
116470
show subpopulations
Gnomad AFR exome
AF:
0.000608
Gnomad AMR exome
AF:
0.00200
Gnomad ASJ exome
AF:
0.00365
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0315
Gnomad FIN exome
AF:
0.00913
Gnomad NFE exome
AF:
0.00570
Gnomad OTH exome
AF:
0.00860
GnomAD4 exome
AF:
0.0105
AC:
15196
AN:
1444138
Hom.:
143
Cov.:
30
AF XY:
0.0112
AC XY:
8011
AN XY:
716374
show subpopulations
Gnomad4 AFR exome
AF:
0.00111
Gnomad4 AMR exome
AF:
0.00210
Gnomad4 ASJ exome
AF:
0.00483
Gnomad4 EAS exome
AF:
0.0000513
Gnomad4 SAS exome
AF:
0.0386
Gnomad4 FIN exome
AF:
0.0133
Gnomad4 NFE exome
AF:
0.00946
Gnomad4 OTH exome
AF:
0.00926
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00775
AC:
1181
AN:
152306
Hom.:
19
Cov.:
33
AF XY:
0.00794
AC XY:
591
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.00168
Gnomad4 AMR
AF:
0.00418
Gnomad4 ASJ
AF:
0.00519
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0423
Gnomad4 FIN
AF:
0.0110
Gnomad4 NFE
AF:
0.00979
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.00731
Hom.:
1
Asia WGS
AF:
0.0240
AC:
82
AN:
3478

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

Splicing

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: rs552710042; hg19: chr7-127292433; API