rs7915642
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001388272.1(SH2D4B):c.988+8554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,086 control chromosomes in the GnomAD database, including 22,147 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 0.52 ( 22147 hom., cov: 32)
Consequence
SH2D4B
NM_001388272.1 intron
NM_001388272.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.22
Genes affected
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D4B | NM_001388272.1 | c.988+8554T>C | intron_variant | ENST00000646907.2 | |||
SH2D4B | NM_001145719.1 | c.841+8554T>C | intron_variant | ||||
SH2D4B | NM_207372.2 | c.985+8554T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D4B | ENST00000646907.2 | c.988+8554T>C | intron_variant | NM_001388272.1 | P1 | ||||
SH2D4B | ENST00000313455.5 | c.841+8554T>C | intron_variant | 2 | |||||
SH2D4B | ENST00000339284.6 | c.985+8554T>C | intron_variant | 2 | |||||
SH2D4B | ENST00000372150.7 | n.330+8554T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.524 AC: 79568AN: 151968Hom.: 22104 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
79568
AN:
151968
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.524 AC: 79665AN: 152086Hom.: 22147 Cov.: 32 AF XY: 0.524 AC XY: 38960AN XY: 74370
GnomAD4 genome
?
AF:
AC:
79665
AN:
152086
Hom.:
Cov.:
32
AF XY:
AC XY:
38960
AN XY:
74370
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:
1784
AN:
3478
ClinVar
Not reported inComputational 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