rs7252505

Positions:

• chr19-33084158-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018025.3(GPATCH1):​c.73+2892G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,146 control chromosomes in the GnomAD database, including 10,705 homozygotes. 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: 𝑓 0.28 (10705 hom., cov: 32)
• Consequence: GPATCH1 NM_018025.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

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]

GPATCH1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPATCH1	NM_018025.3	c.73+2892G>A		intron_variant		ENST00000170564.7	NP_060495.2
GPATCH1	XM_006723255.5	c.73+2892G>A		intron_variant			XP_006723318.1
GPATCH1	NR_135270.2	n.86+2892G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPATCH1	ENST00000170564.7	c.73+2892G>A		intron_variant		1	NM_018025.3	ENSP00000170564.1
GPATCH1	ENST00000592165.1	n.73+2892G>A		intron_variant		5		ENSP00000467632.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42372 AN: 152028 Hom.: 10659 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.216

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.279 AC: 42479 AN: 152146 Hom.: 10705 Cov.: 32 AF XY: 0.279 AC XY: 20778 AN XY: 74392

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0987

Gnomad4 OTH AF: 0.218

Alfa AF: 0.189 Hom.: 1594

Bravo AF: 0.295

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.67

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: rs7252505; hg19: chr19-33575064;