Variant chr7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PM1PM4BP6_ModerateBS1BS2

The NM_014390.4(SND1):c.14_34dup(p.Ala5_Ser11dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,596,444 control chromosomes in the GnomAD database, including 162 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0078 ( 19 hom., cov: 33)

Exomes 𝑓: 0.011 ( 143 hom. )

Consequence

SND1
NM_014390.4 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.70

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PM1

In a modified_residue N-acetylalanine (size 0) in uniprot entity SND1_HUMAN

PM4

Nonframeshift variant in NON repetitive region in NM_014390.4.

BP6

Variant 7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC is Benign according to our data. Variant chr7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC is described in ClinVar as [Benign]. Clinvar id is 718333.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00775 (1181/152306) while in subpopulation SAS AF= 0.0423 (204/4824). AF 95% confidence interval is 0.0375. There are 19 homozygotes in gnomad4. There are 591 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1181 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SND1	NM_014390.4 linkuse as main transcript	c.14_34dup	p.Ala5_Ser11dup	inframe_insertion	1/24	ENST00000354725.8	NP_055205.2
SND1	XM_017011987.3 linkuse as main transcript	c.14_34dup	p.Ala5_Ser11dup	inframe_insertion	1/17		XP_016867476.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SND1	ENST00000354725.8 linkuse as main transcript	c.14_34dup	p.Ala5_Ser11dup	inframe_insertion	1/24	1	NM_014390.4	ENSP00000346762	P1
SND1	ENST00000463020.1 linkuse as main transcript	n.194_214dup		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.00776

AC:

1181

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00169

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0420

Gnomad FIN

AF:

0.0110

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00980

Gnomad OTH

AF:

0.00860

GnomAD3 exomes

AF:

0.00789

AC:

1706

AN:

216140

Hom.:

AF XY:

0.00900

AC XY:

1048

AN XY:

116470

show subpopulations

Gnomad AFR exome

AF:

0.000608

Gnomad AMR exome

AF:

0.00200

Gnomad ASJ exome

AF:

0.00365

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0315

Gnomad FIN exome

AF:

0.00913

Gnomad NFE exome

AF:

0.00570

Gnomad OTH exome

AF:

0.00860

GnomAD4 exome

AF:

0.0105

AC:

15196

AN:

1444138

Hom.:

143

Cov.:

AF XY:

0.0112

AC XY:

8011

AN XY:

716374

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00210

Gnomad4 ASJ exome

AF:

0.00483

Gnomad4 EAS exome

AF:

0.0000513

Gnomad4 SAS exome

AF:

0.0386

Gnomad4 FIN exome

AF:

0.0133

Gnomad4 NFE exome

AF:

0.00946

Gnomad4 OTH exome

AF:

0.00926

GnomAD4 genome

AF:

0.00775

AC:

1181

AN:

152306

Hom.:

Cov.:

AF XY:

0.00794

AC XY:

591

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.00168

Gnomad4 AMR

AF:

0.00418

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0423

Gnomad4 FIN

AF:

0.0110

Gnomad4 NFE

AF:

0.00979

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.00731

Hom.:

Asia WGS

AF:

0.0240

AC:

AN:

3478

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

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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