Variant 2-230462469-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001080391.2(SP100):c.1008C>T(p.Asp336=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,613,734 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0087 ( 8 hom., cov: 31)

Exomes 𝑓: 0.012 ( 131 hom. )

Consequence

SP100
NM_001080391.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.52

Variant links:

Genes affected

SP100 (HGNC:11206): (SP100 nuclear antigen) This gene encodes a subnuclear organelle and major component of the PML (promyelocytic leukemia)-SP100 nuclear bodies. PML and SP100 are covalently modified by the SUMO-1 modifier, which is considered crucial to nuclear body interactions. The encoded protein binds heterochromatin proteins and is thought to play a role in tumorigenesis, immunity, and gene regulation. Alternatively spliced variants have been identified for this gene; one of which encodes a high-mobility group protein. [provided by RefSeq, Aug 2011]

SP100 links:

LOC101928816 (HGNC:):

LOC101928816 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 2-230462469-C-T is Benign according to our data. Variant chr2-230462469-C-T is described in ClinVar as [Benign]. Clinvar id is 771847.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.52 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SP100	NM_001080391.2 linkuse as main transcript	c.1008C>T	p.Asp336=	synonymous_variant	10/29	ENST00000340126.9
LOC101928816	XR_427235.4 linkuse as main transcript	n.472-19104G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP100	ENST00000340126.9 linkuse as main transcript	c.1008C>T	p.Asp336=	synonymous_variant	10/29	1	NM_001080391.2	P1	P23497-4

Frequencies

GnomAD3 genomes

AF:

0.00868

AC:

1320

AN:

152046

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00201

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.00557

Gnomad ASJ

AF:

0.00922

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00540

Gnomad FIN

AF:

0.0184

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0128

Gnomad OTH

AF:

0.00956

GnomAD3 exomes

AF:

0.00908

AC:

2283

AN:

251334

Hom.:

AF XY:

0.00931

AC XY:

1265

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.00203

Gnomad AMR exome

AF:

0.00387

Gnomad ASJ exome

AF:

0.0111

Gnomad EAS exome

AF:

0.000217

Gnomad SAS exome

AF:

0.00497

Gnomad FIN exome

AF:

0.0186

Gnomad NFE exome

AF:

0.0121

Gnomad OTH exome

AF:

0.0111

GnomAD4 exome

AF:

0.0120

AC:

17573

AN:

1461570

Hom.:

131

Cov.:

AF XY:

0.0119

AC XY:

8673

AN XY:

727122

show subpopulations

Gnomad4 AFR exome

AF:

0.00131

Gnomad4 AMR exome

AF:

0.00396

Gnomad4 ASJ exome

AF:

0.00953

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.00489

Gnomad4 FIN exome

AF:

0.0207

Gnomad4 NFE exome

AF:

0.0134

Gnomad4 OTH exome

AF:

0.0103

GnomAD4 genome

AF:

0.00867

AC:

1320

AN:

152164

Hom.:

Cov.:

AF XY:

0.00867

AC XY:

645

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.00200

Gnomad4 AMR

AF:

0.00556

Gnomad4 ASJ

AF:

0.00922

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00541

Gnomad4 FIN

AF:

0.0184

Gnomad4 NFE

AF:

0.0128

Gnomad4 OTH

AF:

0.00946

Alfa

AF:

0.0105

Hom.:

Bravo

AF:

0.00754

Asia WGS

AF:

0.00260

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

Invitae

Jul 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.0

DANN

Benign

0.16

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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