rs373695708

Variant names:

• chr7-99968196-C-A
• rs373695708
• NM_001185.4:c.572G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-99968196-C-A
• chr7-99968196-C-G
• chr7-99968196-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001185.4(AZGP1):​c.572G>T​(p.Arg191Leu) variant causes a missense 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. 13/21 in silico tools predict a benign outcome for this variant. 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. R191Q) 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: -2.64

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

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3305762).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AZGP1	NM_001185.4	c.572G>T	p.Arg191Leu	missense_variant	Exon 3 of 4	ENST00000292401.9	NP_001176.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AZGP1	ENST00000292401.9	c.572G>T	p.Arg191Leu	missense_variant	Exon 3 of 4	1	NM_001185.4	ENSP00000292401.4
AZGP1	ENST00000411734.1	c.563G>T	p.Arg188Leu	missense_variant	Exon 3 of 3	1		ENSP00000396093.1
AZGP1	ENST00000419575.1	c.139-19G>T		intron_variant	Intron 1 of 2	3		ENSP00000389942.1
AZGP1	ENST00000477251.1	n.568G>T		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.090	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	6.2
DANN	Uncertain	0.99
DEOGEN2	Benign	0.18	T;T
Eigen	Benign	-0.72
Eigen_PC	Benign	-0.98
FATHMM_MKL	Benign	0.062	N
LIST_S2	Benign	0.69	T;T
M_CAP	Benign	0.045	D
MetaRNN	Benign	0.33	T;T
MetaSVM	Benign	-0.29	T
MutationAssessor	Benign	1.8	L;.
PrimateAI	Benign	0.24	T
PROVEAN	Pathogenic	-4.9	D;D
REVEL	Uncertain	0.33
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.034	D;D
Polyphen		0.94	P;.
Vest4		0.21
MutPred		0.67		Gain of sheet (P = 0.0149);.;
MVP		0.57
MPC		0.17
ClinPred		0.97	D
GERP RS		-5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.57
gMVP		0.37

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

Other links and lift over

dbSNP: rs373695708; hg19: chr7-99565819;