9-93077980-C-G

Variant names:

• chr9-93077980-C-G
• rs980367427
• NM_145006.4:c.412C>G

Variant summary

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

The NM_145006.4(SUSD3):​c.412C>G​(p.Arg138Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R138W) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SUSD3 NM_145006.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.43
• Publications: 0 publications found

Genes affected

SUSD3 (HGNC:28391): (sushi domain containing 3) Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145006.4. 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
	SUSD3	NM_145006.4	MANE Select	c.412C>G	p.Arg138Gly	missense	Exon 3 of 5	NP_659443.1	Q96L08-1
	SUSD3	NM_001287005.2		c.373C>G	p.Arg125Gly	missense	Exon 4 of 6	NP_001273934.1	Q96L08-2
	SUSD3	NM_001287006.2		c.412C>G	p.Arg138Gly	missense	Exon 3 of 4	NP_001273935.1	A0A087WVN2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUSD3	ENST00000375472.8	TSL:1 MANE Select	c.412C>G	p.Arg138Gly	missense	Exon 3 of 5	ENSP00000364621.3	Q96L08-1
	SUSD3	ENST00000375469.5	TSL:5	c.373C>G	p.Arg125Gly	missense	Exon 3 of 5	ENSP00000364618.1	Q96L08-2
	SUSD3	ENST00000913799.1		c.340C>G	p.Arg114Gly	missense	Exon 4 of 6	ENSP00000583858.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.082	T
BayesDel_noAF	Benign	-0.36
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.20	T
Eigen	Benign	-0.016
Eigen_PC	Benign	-0.15
FATHMM_MKL	Benign	0.30	N
LIST_S2	Uncertain	0.88	D
M_CAP	Benign	0.028	D
MetaRNN	Uncertain	0.45	T
MetaSVM	Benign	-0.70	T
MutationAssessor	Benign	1.8	L
PhyloP100		1.4
PrimateAI	Benign	0.28	T
PROVEAN	Pathogenic	-4.9	D
REVEL	Benign	0.19
Sift	Uncertain	0.0070	D
Sift4G	Uncertain	0.0030	D
Polyphen		0.96	D
Vest4		0.31
MutPred		0.49		Loss of stability (P = 0.0247)
MVP		0.62
MPC		1.2
ClinPred		0.94	D
GERP RS		4.2
PromoterAI		-0.033	Neutral
Varity_R		0.24
gMVP		0.74
Mutation Taster		=82/18	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs980367427; hg19: chr9-95840262;