rs2582717

Variant names:

• chr7-127671809-A-G
• rs2582717
• NM_014390.4:c.79-14804A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-127671809-A-G
• chr7-127671809-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.98).
• 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 rank	MANE	Protein	UniProt
SND1	NM_014390.4	c.79-14804A>G		intron_variant	Intron 1 of 23	ENST00000354725.8	NP_055205.2
SND1	XM_017011987.3	c.79-14804A>G		intron_variant	Intron 1 of 16		XP_016867476.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SND1	ENST00000354725.8	c.79-14804A>G		intron_variant	Intron 1 of 23	1	NM_014390.4	ENSP00000346762.3
SND1	ENST00000463020.1	n.259-14804A>G		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.947 AC: 39319 AN: 41532

American (AMR) AF: 0.756 AC: 11564 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2859 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1789 AN: 5190

South Asian (SAS) AF: 0.664 AC: 3197 AN: 4814

European-Finnish (FIN) AF: 0.667 AC: 7046 AN: 10558

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49880 AN: 68004

Other (OTH) AF: 0.769 AC: 1625 AN: 2112

Alfa AF: 0.752 Hom.: 43176

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
PhyloP100		0.048
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: rs2582717; hg19: chr7-127311863;