chr1-217497185-T-C

Variant names:

• chr1-217497185-T-C
• rs3790728
• NM_018040.5:c.1206+1171A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018040.5(GPATCH2):​c.1206+1171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,106 control chromosomes in the GnomAD database, including 2,095 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 0.11 (2095 hom., cov: 32)
• Consequence: GPATCH2 NM_018040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 2 publications found

Genes affected

GPATCH2 (HGNC:25499): (G-patch domain containing 2) The gene encodes a nuclear factor that may play a role in spermatogenesis and in tumor growth during breast cancer. The encoded protein contains a G-patch domain with an RNA binding motif. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018040.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPATCH2	NM_018040.5	MANE Select	c.1206+1171A>G		intron	N/A	NP_060510.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPATCH2	ENST00000366935.8	TSL:2 MANE Select	c.1206+1171A>G		intron	N/A	ENSP00000355902.3
	GPATCH2	ENST00000470014.6	TSL:3	n.188+1171A>G		intron	N/A
	GPATCH2	ENST00000489246.6	TSL:5	n.409+1171A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17345 AN: 151988 Hom.: 2093 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.0427

Gnomad FIN AF: 0.0177

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0328

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.114 AC: 17367 AN: 152106 Hom.: 2095 Cov.: 32 AF XY: 0.112 AC XY: 8299 AN XY: 74382

African (AFR) AF: 0.309 AC: 12819 AN: 41438

American (AMR) AF: 0.0558 AC: 853 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3470

East Asian (EAS) AF: 0.0869 AC: 450 AN: 5178

South Asian (SAS) AF: 0.0436 AC: 210 AN: 4820

European-Finnish (FIN) AF: 0.0177 AC: 188 AN: 10616

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0328 AC: 2228 AN: 67994

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0500 Hom.: 609

Bravo AF: 0.127

Asia WGS AF: 0.0680 AC: 235 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.77
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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: rs3790728; hg19: chr1-217670527;