rs779566035

Variant names:

• chr12-45925071-G-A
• rs779566035
• NM_004719.3:c.3563C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-45925071-G-A
• chr12-45925071-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004719.3(SCAF11):​c.3563C>T​(p.Ser1188Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. S1188C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SCAF11 NM_004719.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.78

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.106004596).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAF11	NM_004719.3	c.3563C>T	p.Ser1188Phe	missense_variant	Exon 12 of 15	ENST00000369367.8	NP_004710.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAF11	ENST00000369367.8	c.3563C>T	p.Ser1188Phe	missense_variant	Exon 12 of 15	1	NM_004719.3	ENSP00000358374.3
SCAF11	ENST00000549162.5	c.2987C>T	p.Ser996Phe	missense_variant	Exon 6 of 9	1		ENSP00000448864.1
SCAF11	ENST00000465950.5	c.2618C>T	p.Ser873Phe	missense_variant	Exon 2 of 5	1		ENSP00000449812.1
SCAF11	ENST00000547950.1	n.573C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.17	T;.;T
Eigen	Uncertain	0.26
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.91	D;D;D
M_CAP	Benign	0.029	D
MetaRNN	Benign	0.11	T;T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.4	L;.;.
PrimateAI	Benign	0.35	T
PROVEAN	Uncertain	-2.6	D;N;D
REVEL	Benign	0.057
Sift	Uncertain	0.015	D;D;D
Sift4G	Uncertain	0.053	T;T;T
Polyphen		0.98	D;.;.
Vest4		0.20
MutPred		0.26		Gain of sheet (P = 0.0166);.;.;
MVP		0.13
MPC		0.21
ClinPred		0.88	D
GERP RS		3.0
Varity_R		0.13
gMVP		0.22

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

Other links and lift over

dbSNP: rs779566035; hg19: chr12-46318854;