chr19-33108221-T-C

Position:

• chr19-33108221-T-C

Variant summary

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

The NM_018025.3(GPATCH1):​c.1285+1322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,816 control chromosomes in the GnomAD database, including 16,429 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 0.41 (16429 hom., cov: 31)
• Consequence: GPATCH1 NM_018025.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPATCH1	NM_018025.3	c.1285+1322T>C		intron_variant		ENST00000170564.7
GPATCH1	XM_006723255.5	c.1285+1322T>C		intron_variant
GPATCH1	NR_135270.2	n.1298+1322T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPATCH1	ENST00000170564.7	c.1285+1322T>C		intron_variant		1	NM_018025.3	P1
GPATCH1	ENST00000592165.1	c.*741+1322T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62700 AN: 151698 Hom.: 16391 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.414 AC: 62793 AN: 151816 Hom.: 16429 Cov.: 31 AF XY: 0.417 AC XY: 30914 AN XY: 74212

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.379

Alfa AF: 0.290 Hom.: 6161

Bravo AF: 0.430

Asia WGS AF: 0.585 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.49
DANN	Benign	0.35

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: rs10416218; hg19: chr19-33599127;