rs17676986

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014390.4(SND1):​c.1779+5849C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,232 control chromosomes in the GnomAD database, including 1,504 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1504 hom., cov: 32)

Consequence

SND1
NM_014390.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0460
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SND1NM_014390.4 linkuse as main transcriptc.1779+5849C>T intron_variant ENST00000354725.8
SND1XM_017011987.3 linkuse as main transcriptc.1779+5849C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SND1ENST00000354725.8 linkuse as main transcriptc.1779+5849C>T intron_variant 1 NM_014390.4 P1

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
19158
AN:
152114
Hom.:
1499
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0594
Gnomad AMI
AF:
0.117
Gnomad AMR
AF:
0.225
Gnomad ASJ
AF:
0.163
Gnomad EAS
AF:
0.0859
Gnomad SAS
AF:
0.236
Gnomad FIN
AF:
0.121
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.138
Gnomad OTH
AF:
0.129
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.126
AC:
19181
AN:
152232
Hom.:
1504
Cov.:
32
AF XY:
0.129
AC XY:
9631
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0594
Gnomad4 AMR
AF:
0.226
Gnomad4 ASJ
AF:
0.163
Gnomad4 EAS
AF:
0.0857
Gnomad4 SAS
AF:
0.236
Gnomad4 FIN
AF:
0.121
Gnomad4 NFE
AF:
0.138
Gnomad4 OTH
AF:
0.131
Alfa
AF:
0.140
Hom.:
1660
Bravo
AF:
0.129
Asia WGS
AF:
0.176
AC:
609
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
11
DANN
Benign
0.55

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: rs17676986; hg19: chr7-127636958; API