Variant 22-24186073-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000358321.4(SUSD2):c.1397A>G(p.Asn466Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 1,612,152 control chromosomes in the GnomAD database, including 4,729 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.097 ( 907 hom., cov: 33)

Exomes 𝑓: 0.067 ( 3822 hom. )

Consequence

SUSD2
ENST00000358321.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.70

Variant links:

Genes affected

SUSD2 (HGNC:30667): (sushi domain containing 2) Involved in negative regulation of cell cycle G1/S phase transition and negative regulation of cell division. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SUSD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0050433874).

BP6

Variant 22-24186073-A-G is Benign according to our data. Variant chr22-24186073-A-G is described in ClinVar as [Benign]. Clinvar id is 1255298.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUSD2	NM_019601.4 linkuse as main transcript	c.1397A>G	p.Asn466Ser	missense_variant	9/15	ENST00000358321.4	NP_062547.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUSD2	ENST00000358321.4 linkuse as main transcript	c.1397A>G	p.Asn466Ser	missense_variant	9/15	1	NM_019601.4	ENSP00000351075	P1
SUSD2	ENST00000463101.1 linkuse as main transcript	n.2290A>G		non_coding_transcript_exon_variant	7/11	2

Frequencies

GnomAD3 genomes

AF:

0.0965

AC:

14678

AN:

152124

Hom.:

905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.0793

Gnomad ASJ

AF:

0.0663

Gnomad EAS

AF:

0.0783

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.0806

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0619

Gnomad OTH

AF:

0.0938

GnomAD3 exomes

AF:

0.0807

AC:

20110

AN:

249124

Hom.:

981

AF XY:

0.0802

AC XY:

10836

AN XY:

135136

show subpopulations

Gnomad AFR exome

AF:

0.168

Gnomad AMR exome

AF:

0.0764

Gnomad ASJ exome

AF:

0.0700

Gnomad EAS exome

AF:

0.0940

Gnomad SAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.0820

Gnomad NFE exome

AF:

0.0599

Gnomad OTH exome

AF:

0.0745

GnomAD4 exome

AF:

0.0675

AC:

98512

AN:

1459910

Hom.:

3822

Cov.:

AF XY:

0.0692

AC XY:

50213

AN XY:

726120

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.0799

Gnomad4 ASJ exome

AF:

0.0734

Gnomad4 EAS exome

AF:

0.0939

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.0794

Gnomad4 NFE exome

AF:

0.0585

Gnomad4 OTH exome

AF:

0.0699

GnomAD4 genome

AF:

0.0966

AC:

14699

AN:

152242

Hom.:

907

Cov.:

AF XY:

0.0984

AC XY:

7323

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.166

Gnomad4 AMR

AF:

0.0792

Gnomad4 ASJ

AF:

0.0663

Gnomad4 EAS

AF:

0.0787

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.0806

Gnomad4 NFE

AF:

0.0619

Gnomad4 OTH

AF:

0.0923

Alfa

AF:

0.0676

Hom.:

722

Bravo

AF:

0.0983

TwinsUK

AF:

0.0615

AC:

228

ALSPAC

AF:

0.0509

AC:

196

ESP6500AA

AF:

0.169

AC:

744

ESP6500EA

AF:

0.0634

AC:

545

ExAC

AF:

0.0819

AC:

9938

Asia WGS

AF:

0.0910

AC:

317

AN:

3478

EpiCase

AF:

0.0584

EpiControl

AF:

0.0571

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 02, 2020	This variant is associated with the following publications: (PMID: 32620384) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.20

Eigen

Benign

0.059

Eigen_PC

Benign

0.082

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.84

MetaRNN

Benign

0.0050

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

MutationTaster

Benign

0.51

PrimateAI

Benign

0.38

PROVEAN

Uncertain

-4.2

REVEL

Benign

0.17

Sift

Benign

0.19

Sift4G

Benign

0.11

Polyphen

0.57

Vest4

0.086

MPC

0.24

ClinPred

0.046

GERP RS

4.0

Varity_R

0.16

gMVP

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over