rs17107469
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001388272.1(SH2D4B):c.*2406T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0386 in 152,238 control chromosomes in the GnomAD database, including 265 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 0.039 ( 265 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
SH2D4B
NM_001388272.1 3_prime_UTR
NM_001388272.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.71
Genes affected
SH2D4B (HGNC:31440): (SH2 domain containing 4B) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.2).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D4B | NM_001388272.1 | c.*2406T>C | 3_prime_UTR_variant | 8/8 | ENST00000646907.2 | ||
LOC105378387 | XR_946132.1 | n.225+2628A>G | intron_variant, non_coding_transcript_variant | ||||
SH2D4B | NM_001145719.1 | c.*2410T>C | 3_prime_UTR_variant | 7/7 | |||
SH2D4B | NM_207372.2 | c.*2410T>C | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D4B | ENST00000646907.2 | c.*2406T>C | 3_prime_UTR_variant | 8/8 | NM_001388272.1 | P1 | |||
SH2D4B | ENST00000339284.6 | c.*2410T>C | 3_prime_UTR_variant | 7/7 | 2 | ||||
SH2D4B | ENST00000372150.7 | n.2829T>C | non_coding_transcript_exon_variant | 3/3 | 5 | ||||
SH2D4B | ENST00000481537.1 | n.2559T>C | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0386 AC: 5871AN: 152120Hom.: 263 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
5871
AN:
152120
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 Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome ? AF: 0.0386 AC: 5882AN: 152238Hom.: 265 Cov.: 32 AF XY: 0.0367 AC XY: 2735AN XY: 74436
GnomAD4 genome
?
AF:
AC:
5882
AN:
152238
Hom.:
Cov.:
32
AF XY:
AC XY:
2735
AN XY:
74436
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:
64
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