rs3743832
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014117.3(HAPSTR1):c.*3111A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,044 control chromosomes in the GnomAD database, including 22,933 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 0.55 ( 22933 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
HAPSTR1
NM_014117.3 3_prime_UTR
NM_014117.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0240
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=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAPSTR1 | NM_014117.3 | c.*3111A>C | 3_prime_UTR_variant | 4/4 | ENST00000327827.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAPSTR1 | ENST00000327827.12 | c.*3111A>C | 3_prime_UTR_variant | 4/4 | 1 | NM_014117.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.546 AC: 82885AN: 151924Hom.: 22913 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
82885
AN:
151924
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: 0.500 AC: 1AN: 2Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
GnomAD4 exome
AF:
AC:
1
AN:
2
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
2
Gnomad4 NFE exome
AF:
GnomAD4 genome ? AF: 0.545 AC: 82930AN: 152042Hom.: 22933 Cov.: 32 AF XY: 0.545 AC XY: 40499AN XY: 74314
GnomAD4 genome
?
AF:
AC:
82930
AN:
152042
Hom.:
Cov.:
32
AF XY:
AC XY:
40499
AN XY:
74314
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:
1597
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