chr7-127704626-G-A

Variant names:

• chr7-127704626-G-A
• rs1881084
• NM_014390.4:c.841-213G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014390.4(SND1):​c.841-213G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,068 control chromosomes in the GnomAD database, including 9,063 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 0.33 (9063 hom., cov: 32)
• Consequence: SND1 NM_014390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 8 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 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.841-213G>A		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.841-213G>A		intron	N/A	ENSP00000346762.3	Q7KZF4
	SND1	ENST00000903603.1		c.841-213G>A		intron	N/A	ENSP00000573662.1
	SND1	ENST00000915268.1		c.841-213G>A		intron	N/A	ENSP00000585327.1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49672 AN: 151950 Hom.: 9051 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.0826

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.327 AC: 49700 AN: 152068 Hom.: 9063 Cov.: 32 AF XY: 0.321 AC XY: 23889 AN XY: 74332

African (AFR) AF: 0.190 AC: 7898 AN: 41468

American (AMR) AF: 0.419 AC: 6414 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3470

East Asian (EAS) AF: 0.0824 AC: 427 AN: 5184

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4816

European-Finnish (FIN) AF: 0.325 AC: 3431 AN: 10542

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27381 AN: 67980

Other (OTH) AF: 0.361 AC: 763 AN: 2112

Alfa AF: 0.370 Hom.: 4144

Bravo AF: 0.335

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.40
PhyloP100		0.41
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: rs1881084; hg19: chr7-127344680;