rs80215167

Variant names:

• chr9-112063019-C-A
• NM_022486.5:c.1768G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-112063019-C-A
• chr9-112063019-C-T

Variant summary

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

The NM_022486.5(SUSD1):​c.1768G>T​(p.Glu590*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SUSD1 NM_022486.5 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.92

Genes affected

SUSD1 (HGNC:25413): (sushi domain containing 1) Predicted to enable calcium ion binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUSD1	NM_022486.5	c.1768G>T	p.Glu590*	stop_gained	Exon 13 of 17	ENST00000374270.8	NP_071931.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUSD1	ENST00000374270.8	c.1768G>T	p.Glu590*	stop_gained	Exon 13 of 17	1	NM_022486.5	ENSP00000363388.4
SUSD1	ENST00000374264.6	c.1768G>T	p.Glu590*	stop_gained	Exon 13 of 18	1		ENSP00000363382.2
SUSD1	ENST00000374263.7	c.1768G>T	p.Glu590*	stop_gained	Exon 13 of 16	2		ENSP00000363381.3
SUSD1	ENST00000355396.7	c.1717G>T	p.Glu573*	stop_gained	Exon 13 of 16	2		ENSP00000347558.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	40
DANN	Uncertain	0.99
Eigen	Uncertain	0.58
Eigen_PC	Uncertain	0.35
FATHMM_MKL	Uncertain	0.88	D
Vest4		0.17
ClinPred		1.0	D
GERP RS		4.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: chr9-114825299;