chr19-45052872-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_007056.3(CLASRP):​c.279C>T​(p.Thr93Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 1,610,216 control chromosomes in the GnomAD database, including 54 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. Synonymous variant affecting the same amino acid position (i.e. T93T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0056 ( 6 hom., cov: 31)
Exomes 𝑓: 0.0068 ( 48 hom. )

Consequence

CLASRP
NM_007056.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.21
Variant links:
Genes affected
CLASRP (HGNC:17731): (CLK4 associating serine/arginine rich protein) Predicted to be involved in RNA splicing and mRNA processing. Located in nucleoplasm. [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 -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP7
Synonymous conserved (PhyloP=-5.21 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CLASRPNM_007056.3 linkc.279C>T p.Thr93Thr synonymous_variant Exon 4 of 21 ENST00000221455.8 NP_008987.2 Q8N2M8A0A0A0MQS2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CLASRPENST00000221455.8 linkc.279C>T p.Thr93Thr synonymous_variant Exon 4 of 21 1 NM_007056.3 ENSP00000221455.3 A0A0A0MQS2

Frequencies

GnomAD3 genomes
AF:
0.00563
AC:
855
AN:
151964
Hom.:
6
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00128
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0121
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00207
Gnomad FIN
AF:
0.00198
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00824
Gnomad OTH
AF:
0.0120
GnomAD3 exomes
AF:
0.00532
AC:
1309
AN:
245926
Hom.:
8
AF XY:
0.00559
AC XY:
745
AN XY:
133172
show subpopulations
Gnomad AFR exome
AF:
0.000930
Gnomad AMR exome
AF:
0.00815
Gnomad ASJ exome
AF:
0.000515
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00450
Gnomad FIN exome
AF:
0.00187
Gnomad NFE exome
AF:
0.00715
Gnomad OTH exome
AF:
0.00771
GnomAD4 exome
AF:
0.00683
AC:
9958
AN:
1458134
Hom.:
48
Cov.:
31
AF XY:
0.00674
AC XY:
4891
AN XY:
725524
show subpopulations
Gnomad4 AFR exome
AF:
0.00117
Gnomad4 AMR exome
AF:
0.00876
Gnomad4 ASJ exome
AF:
0.000309
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00477
Gnomad4 FIN exome
AF:
0.00262
Gnomad4 NFE exome
AF:
0.00773
Gnomad4 OTH exome
AF:
0.00630
GnomAD4 genome
AF:
0.00562
AC:
855
AN:
152082
Hom.:
6
Cov.:
31
AF XY:
0.00542
AC XY:
403
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.00128
Gnomad4 AMR
AF:
0.0121
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00208
Gnomad4 FIN
AF:
0.00198
Gnomad4 NFE
AF:
0.00824
Gnomad4 OTH
AF:
0.0119
Alfa
AF:
0.00561
Hom.:
4
Bravo
AF:
0.00633
Asia WGS
AF:
0.00144
AC:
5
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
CADD
Benign
0.42
DANN
Benign
0.83

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: rs11667851; hg19: chr19-45556130; COSMIC: COSV99674282; COSMIC: COSV99674282; API