NM_001185.4:c.608G>T

Variant names:

• chr7-99968160-C-A
• rs140596787
• NM_001185.4:c.608G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001185.4(AZGP1):​c.608G>T​(p.Arg203Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R203Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: AZGP1 NM_001185.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 3 publications found

Genes affected

AZGP1 (HGNC:910): (alpha-2-glycoprotein 1, zinc-binding) Involved in cell adhesion and detection of chemical stimulus involved in sensory perception of bitter taste. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001185.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AZGP1	NM_001185.4	MANE Select	c.608G>T	p.Arg203Leu	missense	Exon 3 of 4	NP_001176.1	P25311

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AZGP1	ENST00000292401.9	TSL:1 MANE Select	c.608G>T	p.Arg203Leu	missense	Exon 3 of 4	ENSP00000292401.4	P25311
	AZGP1	ENST00000411734.1	TSL:1	c.599G>T	p.Arg200Leu	missense	Exon 3 of 3	ENSP00000396093.1	C9JEV0
	AZGP1	ENST00000868286.1		c.695G>T	p.Arg232Leu	missense	Exon 4 of 5	ENSP00000538345.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD2 exomes AF: 0.00 AC: 0 AN: 250352 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.040
CADD	Benign	19
DANN	Uncertain	1.0
DEOGEN2	Benign	0.40	T
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.53
FATHMM_MKL	Benign	0.31	N
LIST_S2	Benign	0.68	T
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.66	D
MetaSVM	Uncertain	0.38	D
MutationAssessor	Pathogenic	3.2	M
PhyloP100		0.20
PrimateAI	Benign	0.19	T
PROVEAN	Pathogenic	-5.4	D
REVEL	Uncertain	0.46
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0030	D
Polyphen		0.91	P
Vest4		0.48
MutPred		0.69		Loss of MoRF binding (P = 0.0539)
MVP		0.79
MPC		0.17
ClinPred		0.98	D
GERP RS		0.18
Varity_R		0.67
gMVP		0.47
Mutation Taster		=70/30	polymorphism

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

Other links and lift over

dbSNP: rs140596787; hg19: chr7-99565783;