Variant 22-21208865-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NR_172944.1(GGT2P):n.2119G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00095 ( 10 hom., cov: 15)

Exomes 𝑓: 0.00079 ( 224 hom. )

Failed GnomAD Quality Control

Consequence

GGT2P
NR_172944.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.64

Variant links:

Genes affected

ENSG00000290983 (HGNC:):

ENSG00000290983 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 22-21208865-C-T is Benign according to our data. Variant chr22-21208865-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652936.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GGT2P	NR_172944.1 linkuse as main transcript	n.2119G>A		non_coding_transcript_exon_variant	13/15

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
ENSG00000290983	ENST00000697143.1 linkuse as main transcript	n.1925G>A	non_coding_transcript_exon_variant	11/11
GGT2P	ENST00000697421.1 linkuse as main transcript	n.1338G>A	non_coding_transcript_exon_variant	10/12
ENSG00000290983	ENST00000697422.1 linkuse as main transcript	n.2310G>A	non_coding_transcript_exon_variant	12/14

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

111

AN:

116354

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000883

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00164

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00181

Gnomad OTH

AF:

0.000659

GnomAD3 exomes

AF:

0.00113

AC:

237

AN:

209098

Hom.:

AF XY:

0.00115

AC XY:

132

AN XY:

114502

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000637

Gnomad ASJ exome

AF:

0.000111

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00222

Gnomad NFE exome

AF:

0.00194

Gnomad OTH exome

AF:

0.00229

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000792

AC:

1078

AN:

1360322

Hom.:

224

Cov.:

AF XY:

0.000798

AC XY:

540

AN XY:

676610

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000700

Gnomad4 ASJ exome

AF:

0.000163

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00299

Gnomad4 NFE exome

AF:

0.000829

Gnomad4 OTH exome

AF:

0.00108

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000953

AC:

111

AN:

116430

Hom.:

Cov.:

AF XY:

0.000985

AC XY:

AN XY:

55820

show subpopulations

Gnomad4 AFR

AF:

0.0000881

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00164

Gnomad4 NFE

AF:

0.00181

Gnomad4 OTH

AF:

0.000656

Alfa

AF:

0.000759

Hom.:

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

GGT2P: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.084

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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