chr19-19025732-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001017392.5(SUGP2):​c.616G>A​(p.Gly206Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 1,613,592 control chromosomes in the GnomAD database, including 449,067 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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: 𝑓 0.74 (41181 hom., cov: 28)
  • Exomes 𝑓: 0.75 (407886 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=8.473584E-7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGP2	NM_001017392.5	MANE Select	c.616G>A	p.Gly206Ser	missense	Exon 3 of 11	NP_001017392.2	Q8IX01-1
	SUGP2	NM_001321698.1		c.658G>A	p.Gly220Ser	missense	Exon 3 of 11	NP_001308627.1	M0R2Z9
	SUGP2	NM_001321699.1		c.658G>A	p.Gly220Ser	missense	Exon 3 of 11	NP_001308628.1	M0R2Z9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGP2	ENST00000452918.7	TSL:1 MANE Select	c.616G>A	p.Gly206Ser	missense	Exon 3 of 11	ENSP00000389380.1	Q8IX01-1
	SUGP2	ENST00000337018.10	TSL:1	c.616G>A	p.Gly206Ser	missense	Exon 3 of 11	ENSP00000337926.5	Q8IX01-1
	SUGP2	ENST00000330854.15	TSL:1	n.616G>A		non_coding_transcript_exon	Exon 3 of 13	ENSP00000332373.10	Q8IX01-4

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111487 AN: 151632 Hom.: 41157 Cov.: 28

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.743

GnomAD2 exomes AF: 0.757 AC: 190255 AN: 251372 AF XY: 0.754

Gnomad AFR exome AF: 0.699

Gnomad AMR exome AF: 0.797

Gnomad ASJ exome AF: 0.750

Gnomad EAS exome AF: 0.880

Gnomad FIN exome AF: 0.719

Gnomad NFE exome AF: 0.743

Gnomad OTH exome AF: 0.756

GnomAD4 exome AF: 0.746 AC: 1090716 AN: 1461842 Hom.: 407886 Cov.: 75 AF XY: 0.746 AC XY: 542233 AN XY: 727222

African (AFR) AF: 0.694 AC: 23226 AN: 33478

American (AMR) AF: 0.797 AC: 35658 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 19793 AN: 26136

East Asian (EAS) AF: 0.897 AC: 35628 AN: 39700

South Asian (SAS) AF: 0.747 AC: 64455 AN: 86258

European-Finnish (FIN) AF: 0.724 AC: 38669 AN: 53400

Middle Eastern (MID) AF: 0.734 AC: 4231 AN: 5768

European-Non Finnish (NFE) AF: 0.741 AC: 823817 AN: 1111984

Other (OTH) AF: 0.749 AC: 45239 AN: 60396

GnomAD4 genome AF: 0.735 AC: 111565 AN: 151750 Hom.: 41181 Cov.: 28 AF XY: 0.735 AC XY: 54493 AN XY: 74126

African (AFR) AF: 0.697 AC: 28818 AN: 41326

American (AMR) AF: 0.774 AC: 11780 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2629 AN: 3468

East Asian (EAS) AF: 0.886 AC: 4570 AN: 5156

South Asian (SAS) AF: 0.750 AC: 3601 AN: 4804

European-Finnish (FIN) AF: 0.711 AC: 7484 AN: 10526

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50146 AN: 67946

Other (OTH) AF: 0.741 AC: 1557 AN: 2102

Alfa AF: 0.745 Hom.: 188734

Bravo AF: 0.743

ESP6500AA AF: 0.687 AC: 3028

ESP6500EA AF: 0.743 AC: 6390

ExAC AF: 0.755 AC: 91663

Asia WGS AF: 0.802 AC: 2790 AN: 3478

EpiCase AF: 0.733

EpiControl AF: 0.741

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.055
BayesDel_addAF	Benign	-0.85	T
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.27
DEOGEN2	Benign	0.0021	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.0072	N
LIST_S2	Benign	0.21	T
MetaRNN	Benign	8.5e-7	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.81	N
PhyloP100		-0.080
PrimateAI	Benign	0.37	T
PROVEAN	Benign	0.31	N
REVEL	Benign	0.011
Sift	Benign	1.0	T
Sift4G	Benign	0.81	T
Polyphen		0.0	B
Vest4		0.021
MPC		0.19
ClinPred		0.000017	T
GERP RS		-0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.020
gMVP		0.074
Mutation Taster		=100/0	polymorphism (auto)

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; COSMIC: COSV58258057; COSMIC: COSV58258057;