Variant 5-94629103-T-C 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_032290.4(SLF1):c.126T>C(p.Asn42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00728 in 1,541,018 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0057 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0074 ( 63 hom. )

Consequence

SLF1
NM_032290.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.304

Variant links:

Genes affected

SLF1 (HGNC:25408): (SMC5-SMC6 complex localization factor 1) Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in nucleoplasm and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]

SLF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 5-94629103-T-C is Benign according to our data. Variant chr5-94629103-T-C is described in ClinVar as [Benign]. Clinvar id is 773880.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.304 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 63 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLF1	NM_032290.4 linkuse as main transcript	c.126T>C	p.Asn42=	synonymous_variant	3/21	ENST00000265140.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLF1	ENST00000265140.10 linkuse as main transcript	c.126T>C	p.Asn42=	synonymous_variant	3/21	2	NM_032290.4	P1	Q9BQI6-1

Frequencies

GnomAD3 genomes

AF:

0.00575

AC:

875

AN:

152148

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0153

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00756

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00680

AC:

1020

AN:

149938

Hom.:

AF XY:

0.00729

AC XY:

576

AN XY:

79066

show subpopulations

Gnomad AFR exome

AF:

0.000766

Gnomad AMR exome

AF:

0.00713

Gnomad ASJ exome

AF:

0.00158

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0152

Gnomad FIN exome

AF:

0.00323

Gnomad NFE exome

AF:

0.00732

Gnomad OTH exome

AF:

0.00985

GnomAD4 exome

AF:

0.00744

AC:

10337

AN:

1388752

Hom.:

Cov.:

AF XY:

0.00759

AC XY:

5186

AN XY:

683686

show subpopulations

Gnomad4 AFR exome

AF:

0.00135

Gnomad4 AMR exome

AF:

0.00742

Gnomad4 ASJ exome

AF:

0.00169

Gnomad4 EAS exome

AF:

0.000225

Gnomad4 SAS exome

AF:

0.0143

Gnomad4 FIN exome

AF:

0.00344

Gnomad4 NFE exome

AF:

0.00770

Gnomad4 OTH exome

AF:

0.00684

GnomAD4 genome

AF:

0.00575

AC:

875

AN:

152266

Hom.:

Cov.:

AF XY:

0.00548

AC XY:

408

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00156

Gnomad4 AMR

AF:

0.0107

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0153

Gnomad4 FIN

AF:

0.00292

Gnomad4 NFE

AF:

0.00756

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00488

Hom.:

Bravo

AF:

0.00589

Asia WGS

AF:

0.00520

AC:

AN:

3476

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

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.1

DANN

Benign

0.54

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