7-128089835-T-C

Position:

• chr7-128089835-T-C

Variant summary

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

The NM_014390.4(SND1):​c.2622+143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 773,592 control chromosomes in the GnomAD database, including 170,130 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 0.72 (40436 hom., cov: 32)
  • Exomes 𝑓: 0.64 (129694 hom.)
• Consequence: SND1 NM_014390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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=-0.76).
• 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/exons	MANE	Protein	UniProt
SND1	NM_014390.4	c.2622+143T>C		intron_variant		ENST00000354725.8	NP_055205.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SND1	ENST00000354725.8	c.2622+143T>C		intron_variant		1	NM_014390.4	ENSP00000346762	P1
SND1	ENST00000485871.1	n.337+10T>C		intron_variant, non_coding_transcript_variant		3
SND1	ENST00000489417.5	n.785+143T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108726 AN: 151982 Hom.: 40387 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.711

GnomAD4 exome AF: 0.636 AC: 395438 AN: 621492 Hom.: 129694 Cov.: 8 AF XY: 0.632 AC XY: 200864 AN XY: 317658

Gnomad4 AFR exome AF: 0.917

Gnomad4 AMR exome AF: 0.697

Gnomad4 ASJ exome AF: 0.781

Gnomad4 EAS exome AF: 0.280

Gnomad4 SAS exome AF: 0.582

Gnomad4 FIN exome AF: 0.579

Gnomad4 NFE exome AF: 0.654

Gnomad4 OTH exome AF: 0.662

GnomAD4 genome AF: 0.716 AC: 108832 AN: 152100 Hom.: 40436 Cov.: 32 AF XY: 0.707 AC XY: 52512 AN XY: 74324

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.711

Alfa AF: 0.605 Hom.: 2357

Bravo AF: 0.735

Asia WGS AF: 0.521 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.6
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs322821; hg19: chr7-127729887;