NM_001025159.3:c.-288G>A

Variant names:

• chr5-150413037-C-T
• rs2748249
• NM_001025159.3:c.-288G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001025159.3(CD74):​c.-288G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD74 NM_001025159.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025159.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD74	NM_001025159.3	MANE Select	c.-288G>A		upstream_gene	N/A	NP_001020330.1
	CD74	NM_004355.4		c.-288G>A		upstream_gene	N/A	NP_004346.1
	CD74	NM_001364083.3		c.-288G>A		upstream_gene	N/A	NP_001351012.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD74	ENST00000009530.13	TSL:2 MANE Select	c.-288G>A		upstream_gene	N/A	ENSP00000009530.7
	CD74	ENST00000517791.1	TSL:3	n.-125G>A		upstream_gene	N/A
	CD74	ENST00000523813.2	TSL:4	n.-68G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 915044 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 439958

African (AFR) AF: 0.00 AC: 0 AN: 20970

American (AMR) AF: 0.00 AC: 0 AN: 13360

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13068

East Asian (EAS) AF: 0.00 AC: 0 AN: 22120

South Asian (SAS) AF: 0.00 AC: 0 AN: 46496

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 11504

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2374

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 747884

Other (OTH) AF: 0.00 AC: 0 AN: 37268

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.5
DANN	Benign	0.63
PhyloP100		-0.062
PromoterAI		-0.074	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2748249; hg19: chr5-149792600;