Variant 22-21225471-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NR_172944.1(GGT2P):n.998G>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 0.00011 ( 0 hom., cov: 6)

Exomes 𝑓: 0.00036 ( 16 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: -1.65

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 -2 ACMG points.

BP6

Variant 22-21225471-C-T is Benign according to our data. Variant chr22-21225471-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652944.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.998G>A		non_coding_transcript_exon_variant	5/15

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
ENSG00000290983	ENST00000697143.1 linkuse as main transcript	n.995G>A	non_coding_transcript_exon_variant	5/11
GGT2P	ENST00000697421.1 linkuse as main transcript	n.84G>A	non_coding_transcript_exon_variant	1/12
ENSG00000290983	ENST00000697422.1 linkuse as main transcript	n.1315G>A	non_coding_transcript_exon_variant	5/14

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

64248

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000429

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000758

Gnomad FIN

AF:

0.000276

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000427

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000430

AC:

AN:

72162

Hom.:

AF XY:

0.000459

AC XY:

AN XY:

39242

show subpopulations

Gnomad AFR exome

AF:

0.000194

Gnomad AMR exome

AF:

0.000103

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000326

Gnomad SAS exome

AF:

0.000267

Gnomad FIN exome

AF:

0.00203

Gnomad NFE exome

AF:

0.000364

Gnomad OTH exome

AF:

0.000521

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000364

AC:

157

AN:

430812

Hom.:

Cov.:

AF XY:

0.000340

AC XY:

AN XY:

226240

show subpopulations

Gnomad4 AFR exome

AF:

0.000301

Gnomad4 AMR exome

AF:

0.000180

Gnomad4 ASJ exome

AF:

0.000713

Gnomad4 EAS exome

AF:

0.000165

Gnomad4 SAS exome

AF:

0.000360

Gnomad4 FIN exome

AF:

0.00113

Gnomad4 NFE exome

AF:

0.000300

Gnomad4 OTH exome

AF:

0.000613

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000109

AC:

AN:

64324

Hom.:

Cov.:

AF XY:

0.000192

AC XY:

AN XY:

31288

show subpopulations

Gnomad4 AFR

AF:

0.000128

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000762

Gnomad4 FIN

AF:

0.000276

Gnomad4 NFE

AF:

0.0000427

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000446

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

Oct 01, 2023

ENSG00000290983: BS2; GGT2P: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.18

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.56

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.56

Position offset: -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