Variant 9-112063019-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_022486.5(SUSD1):c.1768G>A(p.Glu590Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00531 in 1,612,074 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0055 ( 28 hom. )

Consequence

SUSD1
NM_022486.5 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.92

Variant links:

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]

SUSD1 links:

SUSD1 (HGNC:):

SUSD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0107268095).

BP6

Variant 9-112063019-C-T is Benign according to our data. Variant chr9-112063019-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 770751.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUSD1	NM_022486.5 linkuse as main transcript	c.1768G>A	p.Glu590Lys	missense_variant	13/17	ENST00000374270.8	NP_071931.2	Q6UWL2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SUSD1	ENST00000374270.8 linkuse as main transcript	c.1768G>A	p.Glu590Lys	missense_variant	13/17	1	NM_022486.5	ENSP00000363388.4	Q6UWL2-1
SUSD1	ENST00000374264.6 linkuse as main transcript	c.1768G>A	p.Glu590Lys	missense_variant	13/18	1		ENSP00000363382.2	Q6UWL2-2
SUSD1	ENST00000374263.7 linkuse as main transcript	c.1768G>A	p.Glu590Lys	missense_variant	13/16	2		ENSP00000363381.3	F8WAQ1
SUSD1	ENST00000355396.7 linkuse as main transcript	c.1717G>A	p.Glu573Lys	missense_variant	13/16	2		ENSP00000347558.3	H3BLV4

Frequencies

GnomAD3 genomes

AF:

0.00322

AC:

490

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000893

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00539

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00581

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00348

AC:

873

AN:

250892

Hom.:

AF XY:

0.00365

AC XY:

495

AN XY:

135638

show subpopulations

Gnomad AFR exome

AF:

0.000862

Gnomad AMR exome

AF:

0.00200

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00480

Gnomad FIN exome

AF:

0.000417

Gnomad NFE exome

AF:

0.00540

Gnomad OTH exome

AF:

0.00344

GnomAD4 exome

AF:

0.00553

AC:

8071

AN:

1459828

Hom.:

Cov.:

AF XY:

0.00549

AC XY:

3989

AN XY:

726372

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00186

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00507

Gnomad4 FIN exome

AF:

0.000656

Gnomad4 NFE exome

AF:

0.00647

Gnomad4 OTH exome

AF:

0.00462

GnomAD4 genome

AF:

0.00322

AC:

490

AN:

152246

Hom.:

Cov.:

AF XY:

0.00278

AC XY:

207

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.000891

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00581

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00579

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00546

Hom.:

Bravo

AF:

0.00305

TwinsUK

AF:

0.00728

AC:

ALSPAC

AF:

0.00778

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00605

AC:

ExAC

AF:

0.00348

AC:

423

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.00616

EpiControl

AF:

0.00552

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	SUSD1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.31

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.049

.;T;.

Eigen

Benign

-0.13

Eigen_PC

Benign

-0.13

FATHMM_MKL

Uncertain

0.84

LIST_S2

Uncertain

0.94

D;D;D

M_CAP

Benign

0.041

MetaRNN

Benign

0.011

T;T;T

MetaSVM

Benign

-0.72

MutationAssessor

Uncertain

2.1

.;M;M

PrimateAI

Uncertain

0.52

PROVEAN

Uncertain

-2.5

D;N;D

REVEL

Benign

0.21

Sift

Benign

0.11

T;T;T

Sift4G

Benign

0.19

T;T;T

Polyphen

0.99

D;D;D

Vest4

0.54

MVP

0.21

MPC

0.72

ClinPred

0.019

GERP RS

4.2

Varity_R

0.16

gMVP

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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