GeneBe

chr9-112087910-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022486.5(SUSD1):​c.1475-7745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,924 control chromosomes in the GnomAD database, including 5,995 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 5995 hom., cov: 32)

Consequence

SUSD1
NM_022486.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.151

Publications

8 publications found
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SUSD1NM_022486.5 linkc.1475-7745G>A intron_variant Intron 10 of 16 ENST00000374270.8 NP_071931.2 Q6UWL2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SUSD1ENST00000374270.8 linkc.1475-7745G>A intron_variant Intron 10 of 16 1 NM_022486.5 ENSP00000363388.4 Q6UWL2-1

Frequencies

GnomAD3 genomes
AF:
0.275
AC:
41800
AN:
151806
Hom.:
5985
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.352
Gnomad AMR
AF:
0.261
Gnomad ASJ
AF:
0.234
Gnomad EAS
AF:
0.222
Gnomad SAS
AF:
0.208
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.324
Gnomad OTH
AF:
0.263
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.275
AC:
41849
AN:
151924
Hom.:
5995
Cov.:
32
AF XY:
0.271
AC XY:
20136
AN XY:
74254
show subpopulations
African (AFR)
AF:
0.220
AC:
9116
AN:
41424
American (AMR)
AF:
0.261
AC:
3993
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.234
AC:
811
AN:
3466
East Asian (EAS)
AF:
0.223
AC:
1150
AN:
5164
South Asian (SAS)
AF:
0.208
AC:
999
AN:
4808
European-Finnish (FIN)
AF:
0.272
AC:
2862
AN:
10538
Middle Eastern (MID)
AF:
0.201
AC:
59
AN:
294
European-Non Finnish (NFE)
AF:
0.324
AC:
21981
AN:
67930
Other (OTH)
AF:
0.265
AC:
558
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1525
3050
4575
6100
7625
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
426
852
1278
1704
2130
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.306
Hom.:
29468
Bravo
AF:
0.272
Asia WGS
AF:
0.224
AC:
777
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.2
DANN
Benign
0.43
PhyloP100
-0.15
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

Publications

Other links and lift over

dbSNP: rs2782931; hg19: chr9-114850190; API