Variant rs10786783 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001002759.2(SFR1):c.56A>G(p.Asp19Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,613,054 control chromosomes in the GnomAD database, including 25,593 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.21 ( 4013 hom., cov: 32)

Exomes 𝑓: 0.17 ( 21580 hom. )

Consequence

SFR1
NM_001002759.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.444

Variant links:

Genes affected

SFR1 (HGNC:29574): (SWI5 dependent homologous recombination repair protein 1) Enables nuclear receptor coactivator activity. Involved in cellular response to estrogen stimulus; double-strand break repair via homologous recombination; and positive regulation of transcription, DNA-templated. Located in nucleus. Part of Swi5-Sfr1 complex. [provided by Alliance of Genome Resources, Apr 2022]

SFR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0039505363).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFR1	NM_001002759.2 linkuse as main transcript	c.56A>G	p.Asp19Gly	missense_variant	2/4	ENST00000369727.4	NP_001002759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFR1	ENST00000369727.4 linkuse as main transcript	c.56A>G	p.Asp19Gly	missense_variant	2/4	2	NM_001002759.2	ENSP00000358742	A1	Q86XK3-1
SFR1	ENST00000369729.7 linkuse as main transcript	c.17A>G	p.Asp6Gly	missense_variant	2/4	1		ENSP00000358744	P4	Q86XK3-3
SFR1	ENST00000463224.5 linkuse as main transcript	n.140A>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32325

AN:

151960

Hom.:

4002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.346

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.201

GnomAD3 exomes

AF:

0.168

AC:

42226

AN:

251156

Hom.:

4065

AF XY:

0.167

AC XY:

22628

AN XY:

135780

show subpopulations

Gnomad AFR exome

AF:

0.350

Gnomad AMR exome

AF:

0.102

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.229

Gnomad SAS exome

AF:

0.171

Gnomad FIN exome

AF:

0.154

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.158

GnomAD4 exome

AF:

0.167

AC:

243460

AN:

1460974

Hom.:

21580

Cov.:

AF XY:

0.166

AC XY:

120814

AN XY:

726816

show subpopulations

Gnomad4 AFR exome

AF:

0.355

Gnomad4 AMR exome

AF:

0.107

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.219

Gnomad4 SAS exome

AF:

0.171

Gnomad4 FIN exome

AF:

0.158

Gnomad4 NFE exome

AF:

0.162

Gnomad4 OTH exome

AF:

0.177

GnomAD4 genome

AF:

0.213

AC:

32359

AN:

152080

Hom.:

4013

Cov.:

AF XY:

0.211

AC XY:

15657

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.346

Gnomad4 AMR

AF:

0.158

Gnomad4 ASJ

AF:

0.118

Gnomad4 EAS

AF:

0.231

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.150

Gnomad4 NFE

AF:

0.159

Gnomad4 OTH

AF:

0.200

Alfa

AF:

0.164

Hom.:

3128

Bravo

AF:

0.220

TwinsUK

AF:

0.174

AC:

644

ALSPAC

AF:

0.164

AC:

631

ESP6500AA

AF:

0.341

AC:

1503

ESP6500EA

AF:

0.159

AC:

1365

ExAC

AF:

0.174

AC:

21078

Asia WGS

AF:

0.239

AC:

830

AN:

3478

EpiCase

AF:

0.155

EpiControl

AF:

0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.011

.;T

Eigen

Benign

-0.66

Eigen_PC

Benign

-0.73

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.57

T;T

MetaRNN

Benign

0.0040

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.0

.;M

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.35

PROVEAN

Benign

-2.3

N;N

REVEL

Benign

0.060

Sift

Benign

0.23

T;T

Sift4G

Benign

0.21

T;T

Polyphen

0.19

.;B

Vest4

0.13

MPC

0.019

ClinPred

0.026

GERP RS

0.86

Varity_R

0.098

gMVP

0.052

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over