7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2

The NM_014390.4(SND1):​c.14_34dupCGCAGAGCGGCGGCTCCTCCG​(p.Ala5_Ser11dup) variant causes a disruptive 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 disruptive_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 Benign. Variant got -8 ACMG points.

PM4
Nonframeshift variant in NON repetitive region in NM_014390.4.
BP6
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
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
High AC in GnomAd4 at 1181 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SND1NM_014390.4 linkc.14_34dupCGCAGAGCGGCGGCTCCTCCG p.Ala5_Ser11dup disruptive_inframe_insertion Exon 1 of 24 ENST00000354725.8 NP_055205.2 Q7KZF4A0A140VK49
SND1XM_017011987.3 linkc.14_34dupCGCAGAGCGGCGGCTCCTCCG p.Ala5_Ser11dup disruptive_inframe_insertion Exon 1 of 17 XP_016867476.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SND1ENST00000354725.8 linkc.14_34dupCGCAGAGCGGCGGCTCCTCCG p.Ala5_Ser11dup disruptive_inframe_insertion Exon 1 of 24 1 NM_014390.4 ENSP00000346762.3 Q7KZF4
SND1ENST00000463020.1 linkn.194_214dupCGCAGAGCGGCGGCTCCTCCG non_coding_transcript_exon_variant Exon 1 of 2 2

Frequencies

GnomAD3 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
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 testingLabcorp Genetics (formerly Invitae), LabcorpDec 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