11-67435917-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_005608.3(PTPRCAP):​c.437G>A​(p.Arg146Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,612,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00060 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00010 ( 0 hom. )

Consequence

PTPRCAP
NM_005608.3 missense

Scores

19

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.401
Variant links:
Genes affected
PTPRCAP (HGNC:9667): (protein tyrosine phosphatase receptor type C associated protein) The protein encoded by this gene was identified as a transmembrane phosphoprotein specifically associated with tyrosine phosphatase PTPRC/CD45, a key regulator of T- and B-lymphocyte activation. The interaction with PTPRC may be required for the stable expression of this protein. [provided by RefSeq, Jul 2008]
CORO1B (HGNC:2253): (coronin 1B) Members of the coronin family, such as CORO1B, are WD repeat-containing actin-binding proteins that regulate cell motility (Cai et al., 2005 [PubMed 16027158]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0069185197).
BP6
Variant 11-67435917-C-T is Benign according to our data. Variant chr11-67435917-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2407360.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTPRCAPNM_005608.3 linkc.437G>A p.Arg146Gln missense_variant Exon 2 of 2 ENST00000326294.4 NP_005599.1 Q14761
CORO1BNM_020441.3 linkc.*2459G>A 3_prime_UTR_variant Exon 11 of 11 ENST00000341356.10 NP_065174.1 Q9BR76A0A024R5K1
CORO1BNM_001018070.3 linkc.*2459G>A 3_prime_UTR_variant Exon 12 of 12 NP_001018080.1 Q9BR76A0A024R5K1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTPRCAPENST00000326294.4 linkc.437G>A p.Arg146Gln missense_variant Exon 2 of 2 1 NM_005608.3 ENSP00000325589.3 Q14761
CORO1BENST00000341356 linkc.*2459G>A 3_prime_UTR_variant Exon 11 of 11 1 NM_020441.3 ENSP00000340211.5 Q9BR76
CORO1BENST00000616321.4 linkn.*3191G>A non_coding_transcript_exon_variant Exon 11 of 11 2 ENSP00000479949.1 A0A087WW53
CORO1BENST00000616321.4 linkn.*3191G>A 3_prime_UTR_variant Exon 11 of 11 2 ENSP00000479949.1 A0A087WW53

Frequencies

GnomAD3 genomes
AF:
0.000591
AC:
90
AN:
152156
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00196
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000327
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000204
AC:
51
AN:
249662
Hom.:
0
AF XY:
0.000177
AC XY:
24
AN XY:
135236
show subpopulations
Gnomad AFR exome
AF:
0.00179
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000545
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.0000466
Gnomad NFE exome
AF:
0.000160
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.000103
AC:
150
AN:
1460588
Hom.:
0
Cov.:
31
AF XY:
0.0000826
AC XY:
60
AN XY:
726610
show subpopulations
Gnomad4 AFR exome
AF:
0.00176
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.0000190
Gnomad4 NFE exome
AF:
0.0000648
Gnomad4 OTH exome
AF:
0.000282
GnomAD4 genome
AF:
0.000598
AC:
91
AN:
152274
Hom.:
0
Cov.:
32
AF XY:
0.000484
AC XY:
36
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.00197
Gnomad4 AMR
AF:
0.000327
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000144
Hom.:
0
Bravo
AF:
0.000688
ESP6500AA
AF:
0.00182
AC:
8
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000272
AC:
33
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Dec 03, 2021
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.061
BayesDel_addAF
Benign
-0.71
T
BayesDel_noAF
Benign
-0.81
CADD
Benign
0.54
DANN
Benign
0.82
DEOGEN2
Benign
0.050
T
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.0039
N
LIST_S2
Benign
0.45
T
M_CAP
Benign
0.0046
T
MetaRNN
Benign
0.0069
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.34
N
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.070
N
REVEL
Benign
0.0030
Sift
Benign
0.54
T
Sift4G
Benign
0.47
T
Polyphen
0.0
B
Vest4
0.043
MVP
0.068
MPC
0.31
ClinPred
0.0022
T
GERP RS
-3.3
Varity_R
0.018
gMVP
0.022

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: rs141177910; hg19: chr11-67203388; API