chr7-128037283-C-T

Variant names:

• chr7-128037283-C-T
• rs6969233
• NM_014390.4:c.1780-37219C>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.1780-37219C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,110 control chromosomes in the GnomAD database, including 40,357 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 0.71 (40357 hom., cov: 31)
• Consequence: SND1 NM_014390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SND1	NM_014390.4	c.1780-37219C>T		intron_variant	Intron 16 of 23	ENST00000354725.8	NP_055205.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SND1	ENST00000354725.8	c.1780-37219C>T		intron_variant	Intron 16 of 23	1	NM_014390.4	ENSP00000346762.3
SND1	ENST00000486037.1	c.427-44077C>T		intron_variant	Intron 4 of 5	3		ENSP00000419327.1
SND1	ENST00000470723.5	n.326+29139C>T		intron_variant	Intron 3 of 4	4
SND1	ENST00000484767.5	n.340-37219C>T		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108636 AN: 151992 Hom.: 40307 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.715 AC: 108742 AN: 152110 Hom.: 40357 Cov.: 31 AF XY: 0.706 AC XY: 52497 AN XY: 74348

African (AFR) AF: 0.914 AC: 37939 AN: 41522

American (AMR) AF: 0.710 AC: 10858 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2741 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1668 AN: 5172

South Asian (SAS) AF: 0.598 AC: 2885 AN: 4822

European-Finnish (FIN) AF: 0.580 AC: 6120 AN: 10552

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44155 AN: 67972

Other (OTH) AF: 0.709 AC: 1497 AN: 2110

Alfa AF: 0.692 Hom.: 4844

Bravo AF: 0.734

Asia WGS AF: 0.524 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.63
PhyloP100		-0.045
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: rs6969233; hg19: chr7-127677336;