rs1368888363

Variant names:

• chr19-49651033-C-A
• NM_021228.3:c.644C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-49651033-C-A
• chr19-49651033-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_021228.3(SCAF1):​c.644C>A​(p.Pro215His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 17)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: SCAF1 NM_021228.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.17235851).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAF1	NM_021228.3	c.644C>A	p.Pro215His	missense_variant	Exon 7 of 11	ENST00000360565.8	NP_067051.2
SCAF1	XM_011527194.4	c.653C>A	p.Pro218His	missense_variant	Exon 7 of 11		XP_011525496.1
SCAF1	XM_005259122.6	c.644C>A	p.Pro215His	missense_variant	Exon 7 of 11		XP_005259179.1
SCAF1	XM_017027083.3	c.374C>A	p.Pro125His	missense_variant	Exon 4 of 8		XP_016882572.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAF1	ENST00000360565.8	c.644C>A	p.Pro215His	missense_variant	Exon 7 of 11	2	NM_021228.3	ENSP00000353769.2
SCAF1	ENST00000598359.5	c.*35C>A		downstream_gene_variant		3		ENSP00000473210.1

Frequencies

GnomAD3 genomes Cov.: 17

GnomAD4 exome AF: 0.00000156 AC: 1 AN: 640218 Hom.: 0 Cov.: 11 AF XY: 0.00000306 AC XY: 1 AN XY: 326974

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: 0.0000190

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 17

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	20
DANN	Benign	0.72
DEOGEN2	Benign	0.038	T
Eigen	Benign	-0.22
Eigen_PC	Benign	-0.34
FATHMM_MKL	Benign	0.21	N
LIST_S2	Benign	0.40	T
M_CAP	Uncertain	0.19	D
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.55	N
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-0.37	N
REVEL	Benign	0.074
Sift	Uncertain	0.0010	D
Sift4G	Benign	0.092	T
Polyphen		0.97	D
Vest4		0.35
MutPred		0.28		Loss of glycosylation at P215 (P = 7e-04);
MVP		0.043
MPC		0.73
ClinPred		0.30	T
GERP RS		3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.12
gMVP		0.20

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: chr19-50154290;