1-217430505-C-T

Position:

• chr1-217430505-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPATCH2	NM_018040.5	c.*640G>A		3_prime_UTR_variant	10/10	ENST00000366935.8	NP_060510.1
GPATCH2	XM_011509689.4	c.*640G>A		3_prime_UTR_variant	11/11		XP_011507991.1
GPATCH2	XM_011509690.4	c.*640G>A		3_prime_UTR_variant	9/9		XP_011507992.1
GPATCH2	XM_017001592.3	c.*640G>A		3_prime_UTR_variant	8/8		XP_016857081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPATCH2	ENST00000366935.8	c.*640G>A		3_prime_UTR_variant	10/10	2	NM_018040.5	ENSP00000355902	P1

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

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.222

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

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.332

Alfa AF: 0.310 Hom.: 12548

Bravo AF: 0.305

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.43
DANN	Benign	0.74

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: rs1048126; hg19: chr1-217603847;