chr16-84907374-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031476.4(CRISPLD2):​c.*732G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,412 control chromosomes in the GnomAD database, including 5,302 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 0.26 ( 5297 hom., cov: 33)
Exomes 𝑓: 0.18 ( 5 hom. )

Consequence

CRISPLD2
NM_031476.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.477
Variant links:
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=-0.84).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CRISPLD2NM_031476.4 linkuse as main transcriptc.*732G>A 3_prime_UTR_variant 15/15 ENST00000262424.10
CRISPLD2XM_005256190.2 linkuse as main transcriptc.*732G>A 3_prime_UTR_variant 16/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRISPLD2ENST00000262424.10 linkuse as main transcriptc.*732G>A 3_prime_UTR_variant 15/151 NM_031476.4 P4Q9H0B8-1
CRISPLD2ENST00000566165.1 linkuse as main transcriptc.121-12266G>A intron_variant, NMD_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.259
AC:
39355
AN:
152032
Hom.:
5281
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.349
Gnomad AMR
AF:
0.338
Gnomad ASJ
AF:
0.240
Gnomad EAS
AF:
0.287
Gnomad SAS
AF:
0.241
Gnomad FIN
AF:
0.211
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.229
Gnomad OTH
AF:
0.292
GnomAD4 exome
AF:
0.179
AC:
47
AN:
262
Hom.:
5
Cov.:
0
AF XY:
0.189
AC XY:
39
AN XY:
206
show subpopulations
Gnomad4 AFR exome
AF:
0.250
Gnomad4 AMR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.375
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.250
Gnomad4 NFE exome
AF:
0.180
Gnomad4 OTH exome
AF:
0.0714
GnomAD4 genome
AF:
0.259
AC:
39409
AN:
152150
Hom.:
5297
Cov.:
33
AF XY:
0.261
AC XY:
19378
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.338
Gnomad4 ASJ
AF:
0.240
Gnomad4 EAS
AF:
0.288
Gnomad4 SAS
AF:
0.240
Gnomad4 FIN
AF:
0.211
Gnomad4 NFE
AF:
0.229
Gnomad4 OTH
AF:
0.289
Alfa
AF:
0.218
Hom.:
2131
Bravo
AF:
0.269
Asia WGS
AF:
0.256
AC:
890
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.8
DANN
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2641670; hg19: chr16-84940980; API