chr4-76436439-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020859.4(SHROOM3):c.168+219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,068 control chromosomes in the GnomAD database, including 8,211 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 8211 hom., cov: 32)
Consequence
SHROOM3
NM_020859.4 intron
NM_020859.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.146
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 4-76436439-T-C is Benign according to our data. Variant chr4-76436439-T-C is described in ClinVar as [Benign]. Clinvar id is 1286515.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM3 | NM_020859.4 | c.168+219T>C | intron_variant | ENST00000296043.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM3 | ENST00000296043.7 | c.168+219T>C | intron_variant | 1 | NM_020859.4 | P1 | |||
SHROOM3 | ENST00000466541.1 | n.75+219T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
SHROOM3 | ENST00000497440.5 | n.109+219T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.304 AC: 46166AN: 151950Hom.: 8205 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.304 AC: 46199AN: 152068Hom.: 8211 Cov.: 32 AF XY: 0.299 AC XY: 22235AN XY: 74334
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?
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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 | Jun 19, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at