19-33088155-T-A

Variant names:

• chr19-33088155-T-A
• NM_018025.3:c.95T>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_018025.3(GPATCH1):​c.95T>A​(p.Ile32Asn) variant causes a missense change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000085 (0 hom., cov: 28)
  • Exomes 𝑓: 0.0010 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GPATCH1 NM_018025.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.51

Genes affected

GPATCH1 (HGNC:24658): (G-patch domain containing 1) Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPATCH1	NM_018025.3	c.95T>A	p.Ile32Asn	missense_variant	Exon 2 of 20	ENST00000170564.7	NP_060495.2
GPATCH1	XM_006723255.5	c.95T>A	p.Ile32Asn	missense_variant	Exon 2 of 14		XP_006723318.1
GPATCH1	NR_135270.2	n.108T>A		non_coding_transcript_exon_variant	Exon 2 of 21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPATCH1	ENST00000170564.7	c.95T>A	p.Ile32Asn	missense_variant	Exon 2 of 20	1	NM_018025.3	ENSP00000170564.1
GPATCH1	ENST00000592165.1	n.95T>A		non_coding_transcript_exon_variant	Exon 2 of 10	5		ENSP00000467632.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 12 AN: 140360 Hom.: 0 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.0000522

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000146

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000457

Gnomad SAS AF: 0.000479

Gnomad FIN AF: 0.000241

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000308

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00102 AC: 996 AN: 972628 Hom.: 0 Cov.: 25 AF XY: 0.000882 AC XY: 438 AN XY: 496750

Gnomad4 AFR exome AF: 0.000618

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000258

Gnomad4 EAS exome AF: 0.000223

Gnomad4 SAS exome AF: 0.000250

Gnomad4 FIN exome AF: 0.000176

Gnomad4 NFE exome AF: 0.00127

Gnomad4 OTH exome AF: 0.00101

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000854 AC: 12 AN: 140472 Hom.: 0 Cov.: 28 AF XY: 0.000147 AC XY: 10 AN XY: 67896

Gnomad4 AFR AF: 0.0000521

Gnomad4 AMR AF: 0.000146

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000457

Gnomad4 SAS AF: 0.000481

Gnomad4 FIN AF: 0.000241

Gnomad4 NFE AF: 0.0000308

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.29	T
Eigen	Benign	0.14
Eigen_PC	Benign	0.093
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.023	T
MetaRNN	Uncertain	0.44	T
MetaSVM	Benign	-1.2	T
MutationAssessor	Uncertain	2.3	M
PrimateAI	Benign	0.37	T
PROVEAN	Pathogenic	-5.2	D
REVEL	Benign	0.12
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0060	D
Polyphen		0.74	P
Vest4		0.51
MutPred		0.38		Gain of relative solvent accessibility (P = 0.0507);
MVP		0.34
MPC		0.52
ClinPred		0.99	D
GERP RS		3.2
Varity_R		0.73
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-33579061;