rs1419970

Variant names:

• chr7-127879225-T-A
• rs1419970
• NM_014390.4:c.1344-8677T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SND1	NM_014390.4	c.1344-8677T>A		intron_variant	Intron 12 of 23	ENST00000354725.8	NP_055205.2
SND1	XM_017011987.3	c.1344-8677T>A		intron_variant	Intron 12 of 16		XP_016867476.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SND1	ENST00000354725.8	c.1344-8677T>A		intron_variant	Intron 12 of 23	1	NM_014390.4	ENSP00000346762.3
SND1	ENST00000465900.5	n.407-8677T>A		intron_variant	Intron 4 of 6	4
SND1	ENST00000468166.5	n.505-8677T>A		intron_variant	Intron 4 of 4	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

African (AFR) AF: 0.125 AC: 5201 AN: 41526

American (AMR) AF: 0.200 AC: 3053 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3468

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5156

South Asian (SAS) AF: 0.0483 AC: 233 AN: 4824

European-Finnish (FIN) AF: 0.216 AC: 2286 AN: 10598

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19284 AN: 67972

Other (OTH) AF: 0.239 AC: 504 AN: 2112

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
PhyloP100		-0.37
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: rs1419970; hg19: chr7-127519278;