Variant chr14-76177923-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_017972.3(GPATCH2L):c.1084C>T(p.Arg362*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00415 in 1,600,232 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0038 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 35 hom. )

Consequence

GPATCH2L
NM_017972.3 stop_gained

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.83

Variant links:

Genes affected

GPATCH2L (HGNC:20210): (G-patch domain containing 2 like)

GPATCH2L links:

GPATCH2L (HGNC:):

GPATCH2L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 14-76177923-C-T is Benign according to our data. Variant chr14-76177923-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644377.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00419 (6061/1448072) while in subpopulation MID AF= 0.0327 (180/5504). AF 95% confidence interval is 0.0288. There are 35 homozygotes in gnomad4_exome. There are 3158 alleles in male gnomad4_exome subpopulation. Median coverage is 28. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPATCH2L	NM_017926.4 linkuse as main transcript	c.1053-65C>T		intron_variant		ENST00000261530.12	NP_060396.2	Q9NWQ4-3A0A024R6E4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPATCH2L	ENST00000261530.12 linkuse as main transcript	c.1053-65C>T		intron_variant		2	NM_017926.4	ENSP00000261530.7		Q9NWQ4-3

Frequencies

GnomAD3 genomes

AF:

0.00383

AC:

583

AN:

152044

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00773

Gnomad ASJ

AF:

0.00952

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00601

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00494

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00469

AC:

1177

AN:

250896

Hom.:

AF XY:

0.00487

AC XY:

661

AN XY:

135614

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.00591

Gnomad ASJ exome

AF:

0.00893

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00628

Gnomad FIN exome

AF:

0.000740

Gnomad NFE exome

AF:

0.00530

Gnomad OTH exome

AF:

0.00816

GnomAD4 exome

AF:

0.00419

AC:

6061

AN:

1448072

Hom.:

Cov.:

AF XY:

0.00438

AC XY:

3158

AN XY:

721430

show subpopulations

Gnomad4 AFR exome

AF:

0.00133

Gnomad4 AMR exome

AF:

0.00618

Gnomad4 ASJ exome

AF:

0.00795

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00603

Gnomad4 FIN exome

AF:

0.000543

Gnomad4 NFE exome

AF:

0.00403

Gnomad4 OTH exome

AF:

0.00623

GnomAD4 genome

AF:

0.00383

AC:

583

AN:

152160

Hom.:

Cov.:

AF XY:

0.00367

AC XY:

273

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00772

Gnomad4 ASJ

AF:

0.00952

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00494

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.00123

Hom.:

Bravo

AF:

0.00431

TwinsUK

AF:

0.00512

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.00182

AC:

ESP6500EA

AF:

0.00442

AC:

ExAC

AF:

0.00443

AC:

538

Asia WGS

AF:

0.00289

AC:

AN:

3476

EpiCase

AF:

0.00578

EpiControl

AF:

0.00878

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

GPATCH2L: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.21

CADD

Uncertain

DANN

Uncertain

1.0

Eigen

Benign

-0.15

Eigen_PC

Benign

-0.059

FATHMM_MKL

Uncertain

0.92

Vest4

0.41

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over