chr4-76436345-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_020859.4(SHROOM3):c.168+125G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,060,848 control chromosomes in the GnomAD database, including 13,019 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 1921 hom., cov: 32)
Exomes 𝑓: 0.15 ( 11098 hom. )
Consequence
SHROOM3
NM_020859.4 intron
NM_020859.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.322
Genes affected
SHROOM3 (HGNC:30422): (shroom family member 3) This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 4-76436345-G-T is Benign according to our data. Variant chr4-76436345-G-T is described in ClinVar as [Benign]. Clinvar id is 1280311.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM3 | NM_020859.4 | c.168+125G>T | intron_variant | ENST00000296043.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM3 | ENST00000296043.7 | c.168+125G>T | intron_variant | 1 | NM_020859.4 | P1 | |||
SHROOM3 | ENST00000466541.1 | n.75+125G>T | intron_variant, non_coding_transcript_variant | 3 | |||||
SHROOM3 | ENST00000497440.5 | n.109+125G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.158 AC: 23966AN: 151826Hom.: 1917 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
23966
AN:
151826
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.151 AC: 137684AN: 908904Hom.: 11098 AF XY: 0.155 AC XY: 72132AN XY: 466872
GnomAD4 exome
AF:
AC:
137684
AN:
908904
Hom.:
AF XY:
AC XY:
72132
AN XY:
466872
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.158 AC: 23973AN: 151944Hom.: 1921 Cov.: 32 AF XY: 0.158 AC XY: 11707AN XY: 74256
GnomAD4 genome
?
AF:
AC:
23973
AN:
151944
Hom.:
Cov.:
32
AF XY:
AC XY:
11707
AN XY:
74256
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
718
AN:
3476
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at