3-101254014-A-G

Variant summary

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

The NM_016247.4(IMPG2):​c.1154-233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,088 control chromosomes in the GnomAD database, including 1,316 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 0.13 ( 1316 hom., cov: 32)

Consequence

IMPG2
NM_016247.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Publications

2 publications found
Variant links:
Genes affected
IMPG2 (HGNC:18362): (interphotoreceptor matrix proteoglycan 2) The protein encoded by this gene binds chondroitin sulfate and hyaluronan and is a proteoglycan. The encoded protein plays a role in the organization of the interphotoreceptor matrix and may promote the growth and maintenance of the light-sensitive photoreceptor outer segment. Defects in this gene are a cause of retinitis pigmentosa type 56 and maculopathy, IMPG2-related.[provided by RefSeq, Mar 2011]
IMPG2 Gene-Disease associations (from GenCC):
  • vitelliform macular dystrophy 5
    Inheritance: AD, Unknown Classification: DEFINITIVE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
  • inherited retinal dystrophy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • retinitis pigmentosa 56
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • adult-onset foveomacular vitelliform dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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=-0.64).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IMPG2NM_016247.4 linkc.1154-233T>C intron_variant Intron 10 of 18 ENST00000193391.8 NP_057331.2 Q9BZV3F1T0J3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IMPG2ENST00000193391.8 linkc.1154-233T>C intron_variant Intron 10 of 18 1 NM_016247.4 ENSP00000193391.6 Q9BZV3

Frequencies

GnomAD3 genomes
AF:
0.128
AC:
19498
AN:
151970
Hom.:
1315
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.113
Gnomad AMI
AF:
0.366
Gnomad AMR
AF:
0.126
Gnomad ASJ
AF:
0.148
Gnomad EAS
AF:
0.164
Gnomad SAS
AF:
0.164
Gnomad FIN
AF:
0.0945
Gnomad MID
AF:
0.171
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.143
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.128
AC:
19501
AN:
152088
Hom.:
1316
Cov.:
32
AF XY:
0.128
AC XY:
9512
AN XY:
74388
show subpopulations
African (AFR)
AF:
0.113
AC:
4701
AN:
41496
American (AMR)
AF:
0.126
AC:
1918
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.148
AC:
513
AN:
3472
East Asian (EAS)
AF:
0.163
AC:
845
AN:
5172
South Asian (SAS)
AF:
0.162
AC:
779
AN:
4822
European-Finnish (FIN)
AF:
0.0945
AC:
1001
AN:
10592
Middle Eastern (MID)
AF:
0.167
AC:
49
AN:
294
European-Non Finnish (NFE)
AF:
0.133
AC:
9060
AN:
67964
Other (OTH)
AF:
0.143
AC:
301
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
908
1816
2725
3633
4541
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
218
436
654
872
1090
<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:
0.134
Hom.:
691
Bravo
AF:
0.128
Asia WGS
AF:
0.181
AC:
626
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
9.6
DANN
Benign
0.92
PhyloP100
1.3
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: rs3732893; hg19: chr3-100972858; API