22-21209102-C-T

Position:

• chr22-21209102-C-T

Variant summary

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

The ENST00000697421.1(GGT2P):​n.1209-6G>A variant causes a splice region, intron 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 0.0039 (0 hom., cov: 5)
  • Exomes 𝑓: 0.0065 (486 hom.)
  • Failed GnomAD Quality Control
• Consequence: GGT2P ENST00000697421.1 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.05

Genes affected

ENSG00000290983 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 22-21209102-C-T is Benign according to our data. Variant chr22-21209102-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652938.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	n.1984G>A		non_coding_transcript_exon_variant	12/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290983	ENST00000697143.1	n.1790G>A		non_coding_transcript_exon_variant	10/11
ENSG00000290983	ENST00000697422.1	n.2175G>A		non_coding_transcript_exon_variant	11/14
GGT2P	ENST00000697421.1	n.1209-6G>A		splice_region_variant, intron_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 106 AN: 26802 Hom.: 0 Cov.: 5 FAILED QC

Gnomad AFR AF: 0.00126

Gnomad AMI AF: 0.0574

Gnomad AMR AF: 0.000429

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00415

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00662

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00416 AC: 254 AN: 61044 Hom.: 26 AF XY: 0.00401 AC XY: 123 AN XY: 30690

Gnomad AFR exome AF: 0.000524

Gnomad AMR exome AF: 0.00126

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000185

Gnomad FIN exome AF: 0.00599

Gnomad NFE exome AF: 0.00876

Gnomad OTH exome AF: 0.00213

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00652 AC: 3085 AN: 472906 Hom.: 486 Cov.: 5 AF XY: 0.00605 AC XY: 1497 AN XY: 247532

Gnomad4 AFR exome AF: 0.00121

Gnomad4 AMR exome AF: 0.00154

Gnomad4 ASJ exome AF: 0.000213

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000302

Gnomad4 FIN exome AF: 0.00916

Gnomad4 NFE exome AF: 0.00898

Gnomad4 OTH exome AF: 0.00520

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00395 AC: 106 AN: 26866 Hom.: 0 Cov.: 5 AF XY: 0.00273 AC XY: 33 AN XY: 12094

Gnomad4 AFR AF: 0.00126

Gnomad4 AMR AF: 0.000427

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00415

Gnomad4 NFE AF: 0.00662

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000510 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2022

GGT2P: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.21		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.21		Position offset: -2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs532427712; hg19: chr22-21563391;