rs1056400

Variant summary

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

The NM_001025159.3(CD74):​c.*176A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,538,994 control chromosomes in the GnomAD database, including 11,109 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 0.083 ( 697 hom., cov: 32)
Exomes 𝑓: 0.12 ( 10412 hom. )

Consequence

CD74
NM_001025159.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.328
Variant links:
Genes affected
CD74 (HGNC:1697): (CD74 molecule) The protein encoded by this gene associates with class II major histocompatibility complex (MHC) and is an important chaperone that regulates antigen presentation for immune response. It also serves as cell surface receptor for the cytokine macrophage migration inhibitory factor (MIF) which, when bound to the encoded protein, initiates survival pathways and cell proliferation. This protein also interacts with amyloid precursor protein (APP) and suppresses the production of amyloid beta (Abeta). Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]

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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD74NM_001025159.3 linkuse as main transcriptc.*176A>G 3_prime_UTR_variant 9/9 ENST00000009530.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD74ENST00000009530.13 linkuse as main transcriptc.*176A>G 3_prime_UTR_variant 9/92 NM_001025159.3 P1P04233-1

Frequencies

GnomAD3 genomes
AF:
0.0835
AC:
12688
AN:
152034
Hom.:
698
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0235
Gnomad AMI
AF:
0.110
Gnomad AMR
AF:
0.0585
Gnomad ASJ
AF:
0.0565
Gnomad EAS
AF:
0.239
Gnomad SAS
AF:
0.0732
Gnomad FIN
AF:
0.101
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.113
Gnomad OTH
AF:
0.0844
GnomAD4 exome
AF:
0.116
AC:
160520
AN:
1386842
Hom.:
10412
Cov.:
32
AF XY:
0.114
AC XY:
78152
AN XY:
684306
show subpopulations
Gnomad4 AFR exome
AF:
0.0200
Gnomad4 AMR exome
AF:
0.0450
Gnomad4 ASJ exome
AF:
0.0578
Gnomad4 EAS exome
AF:
0.283
Gnomad4 SAS exome
AF:
0.0693
Gnomad4 FIN exome
AF:
0.100
Gnomad4 NFE exome
AF:
0.121
Gnomad4 OTH exome
AF:
0.105
GnomAD4 genome
AF:
0.0833
AC:
12679
AN:
152152
Hom.:
697
Cov.:
32
AF XY:
0.0834
AC XY:
6200
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0235
Gnomad4 AMR
AF:
0.0584
Gnomad4 ASJ
AF:
0.0565
Gnomad4 EAS
AF:
0.238
Gnomad4 SAS
AF:
0.0728
Gnomad4 FIN
AF:
0.101
Gnomad4 NFE
AF:
0.113
Gnomad4 OTH
AF:
0.0840
Alfa
AF:
0.103
Hom.:
869
Bravo
AF:
0.0795
Asia WGS
AF:
0.110
AC:
383
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.5
DANN
Benign
0.58
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

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: rs1056400; hg19: chr5-149781627; API