chr2-37092193-A-G

Variant names:

• chr2-37092193-A-G
• rs772033547
• NM_174931.4:c.478A>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_174931.4(GPATCH11):​c.478A>G​(p.Met160Val) 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. 15/19 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. M160L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: GPATCH11 NM_174931.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 0 publications found

Genes affected

GPATCH11 (HGNC:26768): (G-patch domain containing 11) Predicted to enable nucleic acid binding activity. Located in kinetochore. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07083687).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174931.4. 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
	GPATCH11	NM_174931.4	MANE Select	c.478A>G	p.Met160Val	missense	Exon 6 of 9	NP_777591.4	A0A6I8PRS5
	GPATCH11	NM_001371856.3		c.502A>G	p.Met168Val	missense	Exon 6 of 9	NP_001358785.2
	GPATCH11	NM_001371858.3		c.478A>G	p.Met160Val	missense	Exon 6 of 9	NP_001358787.2	A0A6I8PRS5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPATCH11	ENST00000674370.2	MANE Select	c.478A>G	p.Met160Val	missense	Exon 6 of 9	ENSP00000501347.1	A0A6I8PRS5
	GPATCH11	ENST00000281932.6	TSL:1	c.70A>G	p.Met24Val	missense	Exon 4 of 7	ENSP00000281932.6	A0A6Q8JGY2
	GPATCH11	ENST00000964376.1		c.502A>G	p.Met168Val	missense	Exon 6 of 9	ENSP00000634435.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.74
Eigen	Benign	-0.79
Eigen_PC	Benign	-0.64
FATHMM_MKL	Benign	0.72	D
LIST_S2	Benign	0.46	T
M_CAP	Benign	0.0016	T
MetaRNN	Benign	0.071	T
MetaSVM	Benign	-1.0	T
PhyloP100		0.0090
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-1.6	N
REVEL	Benign	0.041
Sift	Benign	0.30	T
Sift4G	Benign	0.21	T
Polyphen		0.0	B
Vest4		0.094
MVP		0.030
ClinPred		0.042	T
GERP RS		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.054
gMVP		0.20
Mutation Taster		=95/5	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: rs772033547; hg19: chr2-37319336;