Variant chr10-29458226-GCTC-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021738.3(SVIL):c.*18_*20del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,611,846 control chromosomes in the GnomAD database, including 11,805 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.095 ( 856 hom., cov: 31)

Exomes 𝑓: 0.12 ( 10949 hom. )

Consequence

SVIL
NM_021738.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.450

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 10-29458226-GCTC-G is Benign according to our data. Variant chr10-29458226-GCTC-G is described in ClinVar as [Benign]. Clinvar id is 1242800.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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.18_20del		3_prime_UTR_variant	38/38	ENST00000355867.9	NP_068506.2
SVIL-AS1	NR_110927.1 linkuse as main transcript	n.182-28925_182-28923del		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.18_20del		3_prime_UTR_variant	38/38	1	NM_021738.3	ENSP00000348128	A2	O95425-1
SVIL-AS1	ENST00000684815.1 linkuse as main transcript	n.236+42818_236+42820del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0948

AC:

14421

AN:

152158

Hom.:

857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0466

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.0848

Gnomad ASJ

AF:

0.0504

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0292

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.0875

GnomAD3 exomes

AF:

0.0886

AC:

22164

AN:

250134

Hom.:

1337

AF XY:

0.0883

AC XY:

11940

AN XY:

135228

show subpopulations

Gnomad AFR exome

AF:

0.0466

Gnomad AMR exome

AF:

0.0457

Gnomad ASJ exome

AF:

0.0555

Gnomad EAS exome

AF:

0.000218

Gnomad SAS exome

AF:

0.0317

Gnomad FIN exome

AF:

0.151

Gnomad NFE exome

AF:

0.128

Gnomad OTH exome

AF:

0.0917

GnomAD4 exome

AF:

0.116

AC:

168882

AN:

1459570

Hom.:

10949

AF XY:

0.113

AC XY:

82210

AN XY:

726226

show subpopulations

Gnomad4 AFR exome

AF:

0.0454

Gnomad4 AMR exome

AF:

0.0484

Gnomad4 ASJ exome

AF:

0.0547

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0316

Gnomad4 FIN exome

AF:

0.153

Gnomad4 NFE exome

AF:

0.132

Gnomad4 OTH exome

AF:

0.103

GnomAD4 genome

AF:

0.0947

AC:

14418

AN:

152276

Hom.:

856

Cov.:

AF XY:

0.0953

AC XY:

7093

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0465

Gnomad4 AMR

AF:

0.0847

Gnomad4 ASJ

AF:

0.0504

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0290

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.0866

Alfa

AF:

0.106

Hom.:

166

Bravo

AF:

0.0881

Asia WGS

AF:

0.0190

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

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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