rs3962697

Positions:

• chr22-21208755-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_172944.1(GGT2P):​n.2200+29C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.000020 (0 hom., cov: 4)
  • Exomes 𝑓: 0.000048 (7 hom.)
  • Failed GnomAD Quality Control
• Consequence: GGT2P NR_172944.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

Genes affected

GGT2P (HGNC:4251): (gamma-glutamyltransferase 2, pseudogene) This gene (GGT2P) appears to be a human duplication of the gamma-glutamyltransferase 1 (GGT1) gene. While GGT2P and GGT1 can potentially encode proteins of the same size and with 94% identity, the ability of GGT2P to encode a stable, functional enzyme has been disputed (see PMID:23682772). Since it is also expressed at a much lower level than GGT1, GGT2P is now thought to be a processed pseudogene. [provided by RefSeq, Jan 2022]

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GGT2P	NR_172944.1	n.2200+29C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GGT2P	ENST00000697421.1	n.1419+29C>G		intron_variant, non_coding_transcript_variant
	ENST00000697422.1	n.2391+29C>G		intron_variant, non_coding_transcript_variant
	ENST00000697143.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1 AN: 48822 Hom.: 0 Cov.: 4 FAILED QC

Gnomad AFR AF: 0.00

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: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000490

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000332 AC: 2 AN: 60178 Hom.: 0 AF XY: 0.0000325 AC XY: 1 AN XY: 30768

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000764

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000482 AC: 38 AN: 788748 Hom.: 7 Cov.: 11 AF XY: 0.0000517 AC XY: 21 AN XY: 405808

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000247

Gnomad4 NFE exome AF: 0.0000602

Gnomad4 OTH exome AF: 0.000113

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000205 AC: 1 AN: 48822 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 22724

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000490

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.69

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

LitVar

Other links and lift over

dbSNP: rs3962697; hg19: chr22-21563044;