Variant chr12-45927731-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000369367.8(SCAF11):c.1970T>A(p.Phe657Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 1,609,834 control chromosomes in the GnomAD database, including 186,367 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.39 ( 13529 hom., cov: 31)

Exomes 𝑓: 0.48 ( 172838 hom. )

Consequence

SCAF11
ENST00000369367.8 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600

Variant links:

Genes affected

SCAF11 (HGNC:10784): (SR-related CTD associated factor 11) Enables RNA binding activity. Involved in spliceosomal complex assembly. Located in nuclear body and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

SCAF11 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=7.763106E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCAF11	NM_004719.3 linkuse as main transcript	c.1970T>A	p.Phe657Tyr	missense_variant	11/15	ENST00000369367.8	NP_004710.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCAF11	ENST00000369367.8 linkuse as main transcript	c.1970T>A	p.Phe657Tyr	missense_variant	11/15	1	NM_004719.3	ENSP00000358374	P1	Q99590-1
SCAF11	ENST00000549162.5 linkuse as main transcript	c.1394T>A	p.Phe465Tyr	missense_variant	5/9	1		ENSP00000448864
SCAF11	ENST00000465950.5 linkuse as main transcript	c.1025T>A	p.Phe342Tyr	missense_variant	1/5	1		ENSP00000449812		Q99590-2
SCAF11	ENST00000547018.5 linkuse as main transcript	c.1790T>A	p.Phe597Tyr	missense_variant	11/11	5		ENSP00000446746

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59706

AN:

151870

Hom.:

13514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.397

Gnomad ASJ

AF:

0.518

Gnomad EAS

AF:

0.544

Gnomad SAS

AF:

0.515

Gnomad FIN

AF:

0.521

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.403

GnomAD3 exomes

AF:

0.463

AC:

115218

AN:

248810

Hom.:

27740

AF XY:

0.474

AC XY:

63727

AN XY:

134578

show subpopulations

Gnomad AFR exome

AF:

0.146

Gnomad AMR exome

AF:

0.413

Gnomad ASJ exome

AF:

0.519

Gnomad EAS exome

AF:

0.548

Gnomad SAS exome

AF:

0.516

Gnomad FIN exome

AF:

0.512

Gnomad NFE exome

AF:

0.481

Gnomad OTH exome

AF:

0.461

GnomAD4 exome

AF:

0.483

AC:

704063

AN:

1457846

Hom.:

172838

Cov.:

AF XY:

0.486

AC XY:

352131

AN XY:

725250

show subpopulations

Gnomad4 AFR exome

AF:

0.146

Gnomad4 AMR exome

AF:

0.409

Gnomad4 ASJ exome

AF:

0.524

Gnomad4 EAS exome

AF:

0.477

Gnomad4 SAS exome

AF:

0.520

Gnomad4 FIN exome

AF:

0.499

Gnomad4 NFE exome

AF:

0.492

Gnomad4 OTH exome

AF:

0.472

GnomAD4 genome

AF:

0.393

AC:

59732

AN:

151988

Hom.:

13529

Cov.:

AF XY:

0.397

AC XY:

29477

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.154

Gnomad4 AMR

AF:

0.397

Gnomad4 ASJ

AF:

0.518

Gnomad4 EAS

AF:

0.546

Gnomad4 SAS

AF:

0.517

Gnomad4 FIN

AF:

0.521

Gnomad4 NFE

AF:

0.489

Gnomad4 OTH

AF:

0.408

Alfa

AF:

0.479

Hom.:

13744

Bravo

AF:

0.375

TwinsUK

AF:

0.499

AC:

1850

ALSPAC

AF:

0.489

AC:

1883

ESP6500AA

AF:

0.165

AC:

729

ESP6500EA

AF:

0.504

AC:

4337

ExAC

AF:

0.456

AC:

55382

Asia WGS

AF:

0.466

AC:

1618

AN:

3472

EpiCase

AF:

0.485

EpiControl

AF:

0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

0.84

DANN

Benign

0.95

DEOGEN2

Benign

0.027

T;.;T

Eigen

Benign

-0.59

Eigen_PC

Benign

-0.68

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.25

T;T;T

MetaRNN

Benign

0.000078

T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.7

L;.;.

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.39

N;N;N

REVEL

Benign

0.021

Sift

Benign

0.055

T;D;D

Sift4G

Benign

0.17

T;T;T

Polyphen

0.67

P;.;P

Vest4

0.086

MPC

0.064

ClinPred

0.0078

GERP RS

1.7

Varity_R

0.035

gMVP

0.041

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over