1-217430505-C-T

Variant names:

• chr1-217430505-C-T
• rs1048126
• NM_018040.5:c.*640G>A

Variant summary

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

The NM_018040.5(GPATCH2):​c.*640G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,014 control chromosomes in the GnomAD database, including 7,309 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 0.30 (7309 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: GPATCH2 NM_018040.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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.*640G>A		3_prime_UTR	Exon 10 of 10	NP_060510.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPATCH2	ENST00000366935.8	TSL:2 MANE Select	c.*640G>A		3_prime_UTR	Exon 10 of 10	ENSP00000355902.3
	GPATCH2	ENST00000885578.1		c.*640G>A		3_prime_UTR	Exon 10 of 10	ENSP00000555637.1
	GPATCH2	ENST00000911527.1		c.*640G>A		3_prime_UTR	Exon 8 of 8	ENSP00000581586.1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46257 AN: 151874 Hom.: 7307 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.250 AC: 5 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.222 AC: 4 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.304 AC: 46272 AN: 151994 Hom.: 7309 Cov.: 32 AF XY: 0.299 AC XY: 22224 AN XY: 74318

African (AFR) AF: 0.355 AC: 14727 AN: 41458

American (AMR) AF: 0.241 AC: 3678 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3466

East Asian (EAS) AF: 0.0909 AC: 470 AN: 5168

South Asian (SAS) AF: 0.297 AC: 1426 AN: 4806

European-Finnish (FIN) AF: 0.221 AC: 2331 AN: 10554

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21478 AN: 67958

Other (OTH) AF: 0.332 AC: 702 AN: 2114

Alfa AF: 0.313 Hom.: 20767

Bravo AF: 0.305

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.43
DANN	Benign	0.74
PhyloP100		-2.8
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: rs1048126; hg19: chr1-217603847;