rs2059397

Variant names:

• chr1-217544790-C-G
• rs2059397
• NM_018040.5:c.1099-29901G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_018040.5(GPATCH2):​c.1099-29901G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 152,298 control chromosomes in the GnomAD database, including 41 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 0.018 (41 hom., cov: 33)
• Consequence: GPATCH2 NM_018040.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.018 (2744/152298) while in subpopulation SAS AF= 0.0351 (169/4820). AF 95% confidence interval is 0.0307. There are 41 homozygotes in gnomad4. There are 1424 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 41 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPATCH2	NM_018040.5	c.1099-29901G>C		intron_variant	Intron 5 of 9	ENST00000366935.8	NP_060510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPATCH2	ENST00000366935.8	c.1099-29901G>C		intron_variant	Intron 5 of 9	2	NM_018040.5	ENSP00000355902.3
GPATCH2	ENST00000470014.6	n.81-29901G>C		intron_variant	Intron 1 of 4	3
GPATCH2	ENST00000485274.1	n.60-29901G>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0180 AC: 2744 AN: 152180 Hom.: 41 Cov.: 33

Gnomad AFR AF: 0.00299

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0180 AC: 2744 AN: 152298 Hom.: 41 Cov.: 33 AF XY: 0.0191 AC XY: 1424 AN XY: 74468

Gnomad4 AFR AF: 0.00298

Gnomad4 AMR AF: 0.0125

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0351

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0221 Hom.: 5

Bravo AF: 0.0146

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.71

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: rs2059397; hg19: chr1-217718132;