7-127682560-C-T

Variant names:

• chr7-127682560-C-T
• rs712707
• NM_014390.4:c.79-4053C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_014390.4(SND1):​c.79-4053C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,102 control chromosomes in the GnomAD database, including 7,260 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 0.28 (7260 hom., cov: 33)
• Consequence: SND1 NM_014390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014390.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SND1	NM_014390.4	MANE Select	c.79-4053C>T		intron	N/A	NP_055205.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SND1	ENST00000354725.8	TSL:1 MANE Select	c.79-4053C>T		intron	N/A	ENSP00000346762.3
	SND1	ENST00000461056.5	TSL:4	n.221+3295C>T		intron	N/A
	SND1	ENST00000463020.1	TSL:2	n.259-4053C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41866 AN: 151984 Hom.: 7257 Cov.: 33

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.275 AC: 41867 AN: 152102 Hom.: 7260 Cov.: 33 AF XY: 0.284 AC XY: 21119 AN XY: 74344

African (AFR) AF: 0.0819 AC: 3401 AN: 41526

American (AMR) AF: 0.278 AC: 4244 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3470

East Asian (EAS) AF: 0.691 AC: 3569 AN: 5164

South Asian (SAS) AF: 0.399 AC: 1928 AN: 4828

European-Finnish (FIN) AF: 0.401 AC: 4227 AN: 10538

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22889 AN: 67986

Other (OTH) AF: 0.277 AC: 586 AN: 2114

Alfa AF: 0.313 Hom.: 1750

Bravo AF: 0.255

Asia WGS AF: 0.495 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	19
DANN	Benign	0.53
PhyloP100		0.81
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: rs712707; hg19: chr7-127322614;