Variant chr10-29458383-GT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000355867.9(SVIL):c.6558+50del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,611,076 control chromosomes in the GnomAD database, including 19,716 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1682 hom., cov: 30)

Exomes 𝑓: 0.15 ( 18034 hom. )

Consequence

SVIL
ENST00000355867.9 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.30

Variant links:

Genes affected

SVIL (HGNC:11480): (supervillin) This gene encodes a bipartite protein with distinct amino- and carboxy-terminal domains. The amino-terminus contains nuclear localization signals and the carboxy-terminus contains numerous consecutive sequences with extensive similarity to proteins in the gelsolin family of actin-binding proteins, which cap, nucleate, and/or sever actin filaments. The gene product is tightly associated with both actin filaments and plasma membranes, suggesting a role as a high-affinity link between the actin cytoskeleton and the membrane. The encoded protein appears to aid in both myosin II assembly during cell spreading and disassembly of focal adhesions. Several transcript variants encoding different isoforms of supervillin have been described. [provided by RefSeq, Apr 2016]

SVIL links:

SVIL-AS1 (HGNC:51219): (SVIL antisense RNA 1)

SVIL-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-29458383-GT-G is Benign according to our data. Variant chr10-29458383-GT-G is described in ClinVar as [Benign]. Clinvar id is 1230829.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SVIL	NM_021738.3 linkuse as main transcript	c.6558+50del		intron_variant		ENST00000355867.9	NP_068506.2
SVIL-AS1	NR_110927.1 linkuse as main transcript	n.182-28771del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SVIL	ENST00000355867.9 linkuse as main transcript	c.6558+50del		intron_variant		1	NM_021738.3	ENSP00000348128	A2	O95425-1
SVIL-AS1	ENST00000684815.1 linkuse as main transcript	n.236+42972del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21597

AN:

152032

Hom.:

1676

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0992

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.299

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.196

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.137

GnomAD3 exomes

AF:

0.162

AC:

39442

AN:

243376

Hom.:

3404

AF XY:

0.162

AC XY:

21280

AN XY:

131476

show subpopulations

Gnomad AFR exome

AF:

0.0984

Gnomad AMR exome

AF:

0.208

Gnomad ASJ exome

AF:

0.0967

Gnomad EAS exome

AF:

0.297

Gnomad SAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.199

Gnomad NFE exome

AF:

0.133

Gnomad OTH exome

AF:

0.155

GnomAD4 exome

AF:

0.152

AC:

221443

AN:

1458926

Hom.:

18034

Cov.:

AF XY:

0.153

AC XY:

110907

AN XY:

725666

show subpopulations

Gnomad4 AFR exome

AF:

0.0967

Gnomad4 AMR exome

AF:

0.216

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.312

Gnomad4 SAS exome

AF:

0.183

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.141

Gnomad4 OTH exome

AF:

0.152

GnomAD4 genome

AF:

0.142

AC:

21615

AN:

152150

Hom.:

1682

Cov.:

AF XY:

0.146

AC XY:

10863

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.0993

Gnomad4 AMR

AF:

0.164

Gnomad4 ASJ

AF:

0.106

Gnomad4 EAS

AF:

0.299

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.196

Gnomad4 NFE

AF:

0.144

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.0892

Hom.:

156

Bravo

AF:

0.138

Asia WGS

AF:

0.229

AC:

792

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

GeneDx

May 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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