rs1419970

Positions:

• chr7-127879225-T-A

Variant summary

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

The NM_014390.4(SND1):​c.1344-8677T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,132 control chromosomes in the GnomAD database, including 3,996 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 0.21 (3996 hom., cov: 32)
• Consequence: SND1 NM_014390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SND1	NM_014390.4	c.1344-8677T>A		intron_variant		ENST00000354725.8
SND1	XM_017011987.3	c.1344-8677T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SND1	ENST00000354725.8	c.1344-8677T>A		intron_variant		1	NM_014390.4	P1
SND1	ENST00000465900.5	n.407-8677T>A		intron_variant, non_coding_transcript_variant		4
SND1	ENST00000468166.5	n.505-8677T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32207 AN: 152014 Hom.: 3998 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.237

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.212 AC: 32209 AN: 152132 Hom.: 3996 Cov.: 32 AF XY: 0.203 AC XY: 15096 AN XY: 74342

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.239

Alfa AF: 0.244 Hom.: 623

Bravo AF: 0.213

Asia WGS AF: 0.0550 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.8
DANN	Benign	0.78

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: rs1419970; hg19: chr7-127519278;