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GeneBe

rs1417938

Variant summary

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

The NM_000567(CRP):c.61+29A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 147286 control chromosomes in the gnomAD Genomes database, including 5405 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 0.25 ( 5405 hom., cov: 27)
Exomes 𝑓: 0.28 ( 10562 hom. )

Consequence

CRP
NM_000567 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CRPNM_000567.3 linkuse as main transcriptc.61+29A>T intron_variant ENST00000255030.9
CRPNM_001329057.2 linkuse as main transcriptc.61+29A>T intron_variant
CRPNM_001329058.2 linkuse as main transcriptc.61+29A>T intron_variant
CRPNM_001382703.1 linkuse as main transcriptc.61+29A>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRPENST00000255030.9 linkuse as main transcriptc.61+29A>T intron_variant 1 NM_000567.3 P1P02741-1

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
37363
AN:
147286
Hom.:
5405
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.122
Gnomad AMI
AF:
0.356
Gnomad AMR
AF:
0.307
Gnomad ASJ
AF:
0.306
Gnomad EAS
AF:
0.0650
Gnomad SAS
AF:
0.250
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.208
Gnomad NFE
AF:
0.314
Gnomad OTH
AF:
0.259
GnomAD3 exomes
AF:
0.279
AC:
69472
AN:
249286
Hom.:
10562
AF XY:
0.278
AC XY:
37496
AN XY:
134802
show subpopulations
Gnomad AFR exome
AF:
0.116
Gnomad AMR exome
AF:
0.368
Gnomad ASJ exome
AF:
0.285
Gnomad EAS exome
AF:
0.0584
Gnomad SAS exome
AF:
0.231
Gnomad FIN exome
AF:
0.350
Gnomad NFE exome
AF:
0.308
Gnomad OTH exome
AF:
0.298
GnomAD4 exome
AF:
0.296
AC:
425804
AN:
1436510
Hom.:
64807
AF XY:
0.295
AC XY:
210864
AN XY:
715426
show subpopulations
Gnomad4 AFR exome
AF:
0.117
Gnomad4 AMR exome
AF:
0.366
Gnomad4 ASJ exome
AF:
0.298
Gnomad4 EAS exome
AF:
0.0693
Gnomad4 SAS exome
AF:
0.234
Gnomad4 FIN exome
AF:
0.358
Gnomad4 NFE exome
AF:
0.310
Gnomad4 OTH exome
AF:
0.276
Alfa
AF:
0.278
Hom.:
1231
Bravo
AF:
0.244
Asia WGS
AF:
0.160
AC:
559
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
4.7
Dann
Benign
0.77

Splicing

Find out SpliceAI 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: rs1417938; hg19: chr1-159684186; COSMIC: COSV54812545; COSMIC: COSV54812545;