rs2582717

chr7-127671809-A-Gchr7-127671809-A-T

Variant summary

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

The NM_014390.4(SND1):c.79-14804A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,174 control chromosomes in the GnomAD database, including 47,224 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 0.78 (47224 hom., cov: 34)
• Consequence: SND1 NM_014390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SND1	NM_014390.4	c.79-14804A>G		intron_variant		ENST00000354725.8
SND1	XM_017011987.3	c.79-14804A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SND1	ENST00000354725.8	c.79-14804A>G		intron_variant		1	NM_014390.4	P1
SND1	ENST00000463020.1	n.259-14804A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118122 AN: 152056 Hom.: 47168 Cov.: 34

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.777 AC: 118234 AN: 152174 Hom.: 47224 Cov.: 34 AF XY: 0.768 AC XY: 57144 AN XY: 74382

Gnomad4 AFR AF: 0.947

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.769

Alfa AF: 0.745 Hom.: 32629

Bravo AF: 0.792

Asia WGS AF: 0.556 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	5.1
Dann	Benign	0.70

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: rs2582717; hg19: chr7-127311863;