rs17151639

Variant names:

• chr7-127997763-A-G
• rs17151639
• NM_014390.4:c.1779+6707A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SND1	NM_014390.4	c.1779+6707A>G		intron_variant	Intron 16 of 23	ENST00000354725.8	NP_055205.2
SND1-IT1	NR_027330.1	n.255A>G		non_coding_transcript_exon_variant	Exon 1 of 1
SND1	XM_017011987.3	c.1779+6707A>G		intron_variant	Intron 16 of 16		XP_016867476.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SND1	ENST00000354725.8	c.1779+6707A>G		intron_variant	Intron 16 of 23	1	NM_014390.4	ENSP00000346762.3

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

GnomAD2 exomes AF: 0.222 AC: 55910 AN: 251360 AF XY: 0.216

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 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

African (AFR) AF: 0.423 AC: 4445 AN: 10512

American (AMR) AF: 0.189 AC: 6874 AN: 36306

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 3773 AN: 11744

East Asian (EAS) AF: 0.0444 AC: 585 AN: 13176

South Asian (SAS) AF: 0.0936 AC: 6246 AN: 66764

European-Finnish (FIN) AF: 0.178 AC: 5741 AN: 32320

Middle Eastern (MID) AF: 0.289 AC: 825 AN: 2854

European-Non Finnish (NFE) AF: 0.260 AC: 49982 AN: 192064

Other (OTH) AF: 0.252 AC: 4215 AN: 16728

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

African (AFR) AF: 0.424 AC: 17580 AN: 41466

American (AMR) AF: 0.255 AC: 3898 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3470

East Asian (EAS) AF: 0.0484 AC: 251 AN: 5188

South Asian (SAS) AF: 0.0903 AC: 435 AN: 4816

European-Finnish (FIN) AF: 0.177 AC: 1874 AN: 10578

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18092 AN: 67992

Other (OTH) AF: 0.310 AC: 654 AN: 2110

Alfa AF: 0.279 Hom.: 13742

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
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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