rs4783099
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_031476.4(CRISPLD2):c.*1081C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,066 control chromosomes in the GnomAD database, including 10,585 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 0.37 ( 10584 hom., cov: 32)
Exomes 𝑓: 0.24 ( 1 hom. )
Consequence
CRISPLD2
NM_031476.4 3_prime_UTR
NM_031476.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.24
Genes affected
CRISPLD2 (HGNC:25248): (cysteine rich secretory protein LCCL domain containing 2) Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRISPLD2 | NM_031476.4 | c.*1081C>T | 3_prime_UTR_variant | 15/15 | ENST00000262424.10 | ||
CRISPLD2 | XM_005256190.2 | c.*1081C>T | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRISPLD2 | ENST00000262424.10 | c.*1081C>T | 3_prime_UTR_variant | 15/15 | 1 | NM_031476.4 | P4 | ||
CRISPLD2 | ENST00000566165.1 | c.121-11917C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.370 AC: 56214AN: 151912Hom.: 10588 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
56214
AN:
151912
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: 0.235 AC: 8AN: 34Hom.: 1 Cov.: 0 AF XY: 0.154 AC XY: 4AN XY: 26
GnomAD4 exome
AF:
AC:
8
AN:
34
Hom.:
Cov.:
0
AF XY:
AC XY:
4
AN XY:
26
Gnomad4 EAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.370 AC: 56235AN: 152032Hom.: 10584 Cov.: 32 AF XY: 0.371 AC XY: 27585AN XY: 74304
GnomAD4 genome
?
AF:
AC:
56235
AN:
152032
Hom.:
Cov.:
32
AF XY:
AC XY:
27585
AN XY:
74304
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:
1509
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