Genetic Variant SND1:c.2622+143T>C (chr7-128089835-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.330

Publications

6 publications found

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 was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SND1	NM_014390.4 link	c.2622+143T>C		intron_variant	Intron 22 of 23	ENST00000354725.8	NP_055205.2	Q7KZF4A0A140VK49

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SND1	ENST00000354725.8 link	c.2622+143T>C	intron_variant	Intron 22 of 23	1	NM_014390.4	ENSP00000346762.3	Q7KZF4
SND1	ENST00000485871.1 link	n.337+10T>C	intron_variant	Intron 1 of 2	3
SND1	ENST00000489417.5 link	n.785+143T>C	intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108726

AN:

151982

Hom.:

40387

Cov.:

show subpopulations

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.:

AF XY:

0.632

AC XY:

200864

AN XY:

317658

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

6621

13242

19864

26485

33106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4392

8784

13176

17568

21960

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.716

AC:

108832

AN:

152100

Hom.:

40436

Cov.:

AF XY:

0.707

AC XY:

52512

AN XY:

74324

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1473

2946

4418

5891

7364

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

806

1612

2418

3224

4030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.6

(source)

DANN

Benign

0.65

PhyloP100

0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over