Menu
GeneBe

19-49650959-C-A

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_021228.3(SCAF1):c.570C>A(p.Pro190=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000475 in 1,535,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., cov: 27)
Exomes 𝑓: 0.000039 ( 0 hom. )

Consequence

SCAF1
NM_021228.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.271
Variant links:
Genes affected
SCAF1 (HGNC:30403): (SR-related CTD associated factor 1) Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-49650959-C-A is Benign according to our data. Variant chr19-49650959-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650276.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.271 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCAF1NM_021228.3 linkuse as main transcriptc.570C>A p.Pro190= synonymous_variant 7/11 ENST00000360565.8
SCAF1XM_011527194.4 linkuse as main transcriptc.579C>A p.Pro193= synonymous_variant 7/11
SCAF1XM_005259122.6 linkuse as main transcriptc.570C>A p.Pro190= synonymous_variant 7/11
SCAF1XM_017027083.3 linkuse as main transcriptc.300C>A p.Pro100= synonymous_variant 4/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCAF1ENST00000360565.8 linkuse as main transcriptc.570C>A p.Pro190= synonymous_variant 7/112 NM_021228.3 P1
SCAF1ENST00000598359.5 linkuse as main transcriptc.570C>A p.Pro190= synonymous_variant 7/73

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000132
AC:
20
AN:
151098
Hom.:
0
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.000389
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000658
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.000486
GnomAD3 exomes
AF:
0.000103
AC:
20
AN:
193432
Hom.:
0
AF XY:
0.0000764
AC XY:
8
AN XY:
104650
show subpopulations
Gnomad AFR exome
AF:
0.000154
Gnomad AMR exome
AF:
0.000333
Gnomad ASJ exome
AF:
0.00100
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000121
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000390
AC:
54
AN:
1384392
Hom.:
0
Cov.:
25
AF XY:
0.0000276
AC XY:
19
AN XY:
687358
show subpopulations
Gnomad4 AFR exome
AF:
0.000284
Gnomad4 AMR exome
AF:
0.000269
Gnomad4 ASJ exome
AF:
0.000552
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000123
Gnomad4 OTH exome
AF:
0.0000696
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000126
AC:
19
AN:
151208
Hom.:
0
Cov.:
27
AF XY:
0.0000812
AC XY:
6
AN XY:
73890
show subpopulations
Gnomad4 AFR
AF:
0.000388
Gnomad4 AMR
AF:
0.0000657
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000481
Alfa
AF:
0.0000434
Hom.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2022SCAF1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
Cadd
Benign
7.3
Dann
Benign
0.75
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.

Other links and lift over

dbSNP: rs373203311; hg19: chr19-50154216; API