19-49646724-C-T

Variant summary

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

The NM_021228.3(SCAF1):​c.372C>T​(p.Asp124Asp) 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 1,461,662 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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.61
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 (BayesDel_noAF=-0.43).
BP7
Synonymous conserved (PhyloP=1.61 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCAF1NM_021228.3 linkc.372C>T p.Asp124Asp synonymous_variant Exon 6 of 11 ENST00000360565.8 NP_067051.2 Q9H7N4
SCAF1XM_011527194.4 linkc.381C>T p.Asp127Asp synonymous_variant Exon 6 of 11 XP_011525496.1
SCAF1XM_005259122.6 linkc.372C>T p.Asp124Asp synonymous_variant Exon 6 of 11 XP_005259179.1 Q9H7N4
SCAF1XM_017027083.3 linkc.102C>T p.Asp34Asp synonymous_variant Exon 3 of 8 XP_016882572.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCAF1ENST00000360565.8 linkc.372C>T p.Asp124Asp synonymous_variant Exon 6 of 11 2 NM_021228.3 ENSP00000353769.2 Q9H7N4
SCAF1ENST00000598359.5 linkc.372C>T p.Asp124Asp synonymous_variant Exon 6 of 7 3 ENSP00000473210.1 M0R3G4
SCAF1ENST00000595242.3 linkc.*105C>T downstream_gene_variant 3 ENSP00000472276.1 M0R232
SCAF1ENST00000601038.5 linkc.*166C>T downstream_gene_variant 3 ENSP00000472649.1 M0R2L3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461662
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
727150
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:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
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_noAF
Benign
-0.43
CADD
Benign
11
DANN
Benign
0.70
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-50149981; API