Variant chr7-127701159-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_014390.4(SND1):c.429-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00256 in 1,613,262 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0026 ( 11 hom. )

Consequence

SND1
NM_014390.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.001688

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.710

Variant links:

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]

SND1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 7-127701159-C-T is Benign according to our data. Variant chr7-127701159-C-T is described in ClinVar as [Benign]. Clinvar id is 709901.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 289 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SND1	NM_014390.4 linkuse as main transcript	c.429-4C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000354725.8	NP_055205.2
SND1	XM_017011987.3 linkuse as main transcript	c.429-4C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			XP_016867476.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
SND1	ENST00000354725.8 linkuse as main transcript	c.429-4C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_014390.4	ENSP00000346762	P1
SND1	ENST00000468621.5 linkuse as main transcript	n.444-4C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	4
SND1	ENST00000483503.5 linkuse as main transcript	n.324-4C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	5
SND1	ENST00000492772.1 linkuse as main transcript	n.236-4C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	4

Frequencies

GnomAD3 genomes

AF:

0.00190

AC:

289

AN:

151924

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000363

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00865

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00228

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00297

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00243

AC:

609

AN:

250800

Hom.:

AF XY:

0.00255

AC XY:

345

AN XY:

135544

show subpopulations

Gnomad AFR exome

AF:

0.000431

Gnomad AMR exome

AF:

0.000203

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00206

Gnomad FIN exome

AF:

0.00273

Gnomad NFE exome

AF:

0.00305

Gnomad OTH exome

AF:

0.00278

GnomAD4 exome

AF:

0.00263

AC:

3841

AN:

1461220

Hom.:

Cov.:

AF XY:

0.00265

AC XY:

1929

AN XY:

726904

show subpopulations

Gnomad4 AFR exome

AF:

0.000359

Gnomad4 AMR exome

AF:

0.000202

Gnomad4 ASJ exome

AF:

0.0111

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00244

Gnomad4 FIN exome

AF:

0.00290

Gnomad4 NFE exome

AF:

0.00271

Gnomad4 OTH exome

AF:

0.00240

GnomAD4 genome

AF:

0.00190

AC:

289

AN:

152042

Hom.:

Cov.:

AF XY:

0.00176

AC XY:

131

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.000362

Gnomad4 AMR

AF:

0.000262

Gnomad4 ASJ

AF:

0.00865

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00228

Gnomad4 NFE

AF:

0.00297

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00299

Hom.:

Bravo

AF:

0.00164

Asia WGS

AF:

0.00115

AC:

AN:

3476

EpiCase

AF:

0.00267

EpiControl

AF:

0.00202

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

9.9

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0017

dbscSNV1_RF

Benign

0.074

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over