rs4808907

Variant names:

• chr19-19025732-C-A
• rs4808907
• NM_001017392.5:c.616G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-19025732-C-A
• chr19-19025732-C-G
• chr19-19025732-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001017392.5(SUGP2):​c.616G>T​(p.Gly206Cys) 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. 15/22 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: 28)
• Consequence: SUGP2 NM_001017392.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 41 publications found

Genes affected

SUGP2 (HGNC:18641): (SURP and G-patch domain containing 2) This gene encodes a member of the arginine/serine-rich family of splicing factors. The encoded protein functions in mRNA processing. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07968688).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017392.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGP2	NM_001017392.5	MANE Select	c.616G>T	p.Gly206Cys	missense	Exon 3 of 11	NP_001017392.2
	SUGP2	NM_001321698.1		c.658G>T	p.Gly220Cys	missense	Exon 3 of 11	NP_001308627.1
	SUGP2	NM_001321699.1		c.658G>T	p.Gly220Cys	missense	Exon 3 of 11	NP_001308628.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGP2	ENST00000452918.7	TSL:1 MANE Select	c.616G>T	p.Gly206Cys	missense	Exon 3 of 11	ENSP00000389380.1
	SUGP2	ENST00000337018.10	TSL:1	c.616G>T	p.Gly206Cys	missense	Exon 3 of 11	ENSP00000337926.5
	SUGP2	ENST00000330854.15	TSL:1	n.616G>T		non_coding_transcript_exon	Exon 3 of 13	ENSP00000332373.10

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Cov.: 75

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0059	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.070	N
LIST_S2	Benign	0.48	T
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.080	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.080
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.93	N
REVEL	Benign	0.13
Sift	Uncertain	0.023	D
Sift4G	Uncertain	0.051	T
Polyphen		0.95	P
Vest4		0.14
MutPred		0.28		Loss of sheet (P = 0.0181)
MVP		0.043
MPC		0.46
ClinPred		0.30	T
GERP RS		-0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.10
gMVP		0.11
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs4808907; hg19: chr19-19136541;