rs151036254

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_021228.3(SCAF1):​c.352C>A​(p.Arg118Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

SCAF1
NM_021228.3 synonymous

Scores

2
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.70
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.26030725).
BP7
Synonymous conserved (PhyloP=1.7 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCAF1NM_021228.3 linkc.352C>A p.Arg118Arg synonymous_variant Exon 5 of 11 ENST00000360565.8 NP_067051.2 Q9H7N4
SCAF1XM_011527194.4 linkc.361C>A p.Arg121Arg synonymous_variant Exon 5 of 11 XP_011525496.1
SCAF1XM_005259122.6 linkc.352C>A p.Arg118Arg synonymous_variant Exon 5 of 11 XP_005259179.1 Q9H7N4
SCAF1XM_017027083.3 linkc.82C>A p.Arg28Arg synonymous_variant Exon 2 of 8 XP_016882572.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCAF1ENST00000360565.8 linkc.352C>A p.Arg118Arg synonymous_variant Exon 5 of 11 2 NM_021228.3 ENSP00000353769.2 Q9H7N4
SCAF1ENST00000595242.3 linkc.356C>A p.Ala119Glu missense_variant Exon 4 of 4 3 ENSP00000472276.1 M0R232
SCAF1ENST00000598359.5 linkc.352C>A p.Arg118Arg synonymous_variant Exon 5 of 7 3 ENSP00000473210.1 M0R3G4
SCAF1ENST00000601038.5 linkc.*58C>A downstream_gene_variant 3 ENSP00000472649.1 M0R2L3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461730
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.023
T
BayesDel_noAF
Benign
-0.20
CADD
Benign
12
DANN
Benign
0.72
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.22
T
MetaRNN
Benign
0.26
T
MVP
0.76
GERP RS
4.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-50149873; API