Genetic Variant NM_174931.4:c.*54G>C (chr2-37096317-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Publications

8 publications found

Variant links:

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]

GPATCH11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 61 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174931.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GPATCH11	NM_174931.4	MANE Select	c.*54G>C	3_prime_UTR	Exon 9 of 9	NP_777591.4	A0A6I8PRS5
GPATCH11	NM_001371856.3		c.*54G>C	3_prime_UTR	Exon 9 of 9	NP_001358785.2
GPATCH11	NM_001371858.3		c.*54G>C	3_prime_UTR	Exon 9 of 9	NP_001358787.2	A0A6I8PRS5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GPATCH11	ENST00000674370.2	MANE Select	c.*54G>C	3_prime_UTR	Exon 9 of 9	ENSP00000501347.1	A0A6I8PRS5
GPATCH11	ENST00000281932.6	TSL:1	c.*54G>C	3_prime_UTR	Exon 7 of 7	ENSP00000281932.6	A0A6Q8JGY2
GPATCH11	ENST00000964376.1		c.*54G>C	3_prime_UTR	Exon 9 of 9	ENSP00000634435.1

Frequencies

GnomAD3 genomes

AF:

0.0227

AC:

3454

AN:

152138

Hom.:

Cov.:

show subpopulations

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.:

AF XY:

0.0300

AC XY:

15178

AN XY:

505988

show subpopulations

African (AFR)

AF:

0.00608

AC:

137

AN:

22516

American (AMR)

AF:

0.0157

AC:

382

AN:

24360

Ashkenazi Jewish (ASJ)

AF:

0.0333

AC:

720

AN:

21642

East Asian (EAS)

AF:

0.000352

AC:

AN:

34096

South Asian (SAS)

AF:

0.0386

AC:

2480

AN:

64222

European-Finnish (FIN)

AF:

0.0241

AC:

1198

AN:

49702

Middle Eastern (MID)

AF:

0.0373

AC:

129

AN:

3460

European-Non Finnish (NFE)

AF:

0.0312

AC:

22690

AN:

727828

Other (OTH)

AF:

0.0268

AC:

1180

AN:

44062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1319

2638

3956

5275

6594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0227

AC:

3453

AN:

152256

Hom.:

Cov.:

AF XY:

0.0218

AC XY:

1624

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.00724

AC:

301

AN:

41548

American (AMR)

AF:

0.0189

AC:

289

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0306

AC:

106

AN:

3468

East Asian (EAS)

AF:

0.000963

AC:

AN:

5192

South Asian (SAS)

AF:

0.0311

AC:

150

AN:

4826

European-Finnish (FIN)

AF:

0.0255

AC:

270

AN:

10596

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0323

AC:

2200

AN:

68022

Other (OTH)

AF:

0.0237

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

167

334

501

668

835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0285

Hom.:

Bravo

AF:

0.0215

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.38

(source)

DANN

Benign

0.39

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over