rs17151639

chr7-127997763-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014390.4(SND1):c.1779+6707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 534,584 control chromosomes in the GnomAD database, including 17,633 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 0.29 (7261 hom., cov: 32)
  • Exomes 𝑓: 0.22 (10372 hom.)
• Consequence: SND1 NM_014390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

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]

SND1-IT1 (HGNC:24158): (SND1 intronic transcript 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SND1	NM_014390.4	c.1779+6707A>G		intron_variant		ENST00000354725.8
SND1-IT1	NR_027330.1	n.255A>G		non_coding_transcript_exon_variant	1/1
SND1	XM_017011987.3	c.1779+6707A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SND1	ENST00000354725.8	c.1779+6707A>G		intron_variant		1	NM_014390.4	P1
SND1-IT1	ENST00000623342.1	n.167A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44370 AN: 151998 Hom.: 7257 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.309

GnomAD3 exomes AF: 0.222 AC: 55910 AN: 251360 Hom.: 7441 AF XY: 0.216 AC XY: 29294 AN XY: 135850

Gnomad AFR exome AF: 0.429

Gnomad AMR exome AF: 0.190

Gnomad ASJ exome AF: 0.322

Gnomad EAS exome AF: 0.0429

Gnomad SAS exome AF: 0.0933

Gnomad FIN exome AF: 0.177

Gnomad NFE exome AF: 0.265

Gnomad OTH exome AF: 0.255

GnomAD4 exome AF: 0.216 AC: 82686 AN: 382468 Hom.: 10372 Cov.: 0 AF XY: 0.206 AC XY: 44814 AN XY: 217724

Gnomad4 AFR exome AF: 0.423

Gnomad4 AMR exome AF: 0.189

Gnomad4 ASJ exome AF: 0.321

Gnomad4 EAS exome AF: 0.0444

Gnomad4 SAS exome AF: 0.0936

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.260

Gnomad4 OTH exome AF: 0.252

GnomAD4 genome AF: 0.292 AC: 44399 AN: 152116 Hom.: 7261 Cov.: 32 AF XY: 0.281 AC XY: 20865 AN XY: 74378

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.0903

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.310

Alfa AF: 0.286 Hom.: 5013

Bravo AF: 0.309

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.28
Dann	Benign	0.24

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

Other links and lift over

dbSNP: rs17151639; hg19: chr7-127637816; COSMIC: COSV61242103;