rs12474977

chr2-37096317-G-C

Variant summary

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

The NM_174931.4(GPATCH11):c.*54G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0283 in 1,144,144 control chromosomes in the GnomAD database, including 541 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 0.023 (61 hom., cov: 33)
  • Exomes 𝑓: 0.029 (480 hom.)
• Consequence: GPATCH11 NM_174931.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

GPATCH11 (HGNC:26768): (G-patch domain containing 11) Predicted to enable nucleic acid binding activity. Located in kinetochore. [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=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0227 (3453/152256) while in subpopulation NFE AF= 0.0323 (2200/68022). AF 95% confidence interval is 0.0312. There are 61 homozygotes in gnomad4. There are 1624 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 61 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPATCH11	NM_174931.4	c.*54G>C		3_prime_UTR_variant	9/9	ENST00000674370.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPATCH11	ENST00000674370.2	c.*54G>C		3_prime_UTR_variant	9/9		NM_174931.4	P1
GPATCH11	ENST00000281932.6	c.*54G>C		3_prime_UTR_variant	7/7	1

Frequencies

GnomAD3 genomes AF: 0.0227 AC: 3454 AN: 152138 Hom.: 61 Cov.: 33

Gnomad AFR AF: 0.00727

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0244

GnomAD4 exome AF: 0.0292 AC: 28928 AN: 991888 Hom.: 480 Cov.: 13 AF XY: 0.0300 AC XY: 15178 AN XY: 505988

Gnomad4 AFR exome AF: 0.00608

Gnomad4 AMR exome AF: 0.0157

Gnomad4 ASJ exome AF: 0.0333

Gnomad4 EAS exome AF: 0.000352

Gnomad4 SAS exome AF: 0.0386

Gnomad4 FIN exome AF: 0.0241

Gnomad4 NFE exome AF: 0.0312

Gnomad4 OTH exome AF: 0.0268

GnomAD4 genome AF: 0.0227 AC: 3453 AN: 152256 Hom.: 61 Cov.: 33 AF XY: 0.0218 AC XY: 1624 AN XY: 74450

Gnomad4 AFR AF: 0.00724

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.0306

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0255

Gnomad4 NFE AF: 0.0323

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0285 Hom.: 14

Bravo AF: 0.0215

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.38
Dann	Benign	0.39

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: rs12474977; hg19: chr2-37323460;