chr7-128089835-T-C

Variant names:

• chr7-128089835-T-C
• rs322821
• NM_014390.4:c.2622+143T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SND1	NM_014390.4	MANE Select	c.2622+143T>C		intron	N/A	NP_055205.2	Q7KZF4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SND1	ENST00000354725.8	TSL:1 MANE Select	c.2622+143T>C		intron	N/A	ENSP00000346762.3	Q7KZF4
	SND1	ENST00000903603.1		c.2805+143T>C		intron	N/A	ENSP00000573662.1
	SND1	ENST00000915268.1		c.2712+143T>C		intron	N/A	ENSP00000585327.1

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

African (AFR) AF: 0.917 AC: 14260 AN: 15546

American (AMR) AF: 0.697 AC: 13662 AN: 19608

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 11402 AN: 14604

East Asian (EAS) AF: 0.280 AC: 8850 AN: 31574

South Asian (SAS) AF: 0.582 AC: 27571 AN: 47348

European-Finnish (FIN) AF: 0.579 AC: 22969 AN: 39654

Middle Eastern (MID) AF: 0.731 AC: 1799 AN: 2460

European-Non Finnish (NFE) AF: 0.654 AC: 274295 AN: 419548

Other (OTH) AF: 0.662 AC: 20630 AN: 31150

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

African (AFR) AF: 0.914 AC: 37964 AN: 41532

American (AMR) AF: 0.710 AC: 10854 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2752 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1662 AN: 5166

South Asian (SAS) AF: 0.599 AC: 2886 AN: 4820

European-Finnish (FIN) AF: 0.576 AC: 6088 AN: 10572

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44249 AN: 67944

Other (OTH) AF: 0.711 AC: 1498 AN: 2108

Alfa AF: 0.624 Hom.: 2670

Bravo AF: 0.735

Asia WGS AF: 0.521 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.6
DANN	Benign	0.65
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs322821; hg19: chr7-127729887; COSMIC: COSV107421139; COSMIC: COSV107421139;