Variant chr7-38349487-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000390344.2(TRGV5):c.222G>T(p.Lys74Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000447 in 713,588 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00040 ( 9 hom., cov: 22)

Exomes 𝑓: 0.00046 ( 51 hom. )

Consequence

TRGV5
ENST00000390344.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.424

Variant links:

Genes affected

TRGV5 (HGNC:12290): (T cell receptor gamma variable 5) Predicted to be involved in adaptive immune response and innate immune response. Predicted to be part of T cell receptor complex. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TRGV5 links:

TRGV5 (HGNC:):

TRGV5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 7-38349487-C-A is Benign according to our data. Variant chr7-38349487-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657387.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons
TRGV5	unassigned_transcript_1236 use as main transcript	c.222G>T	p.Lys74Asn	missense_variant	2/2
TRG	use as main transcript	n.38349487C>A		intragenic_variant
TRG-AS1	NR_040085.1 linkuse as main transcript	n.331-859C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRGV5	ENST00000390344.2 linkuse as main transcript	c.222G>T	p.Lys74Asn	missense_variant	2/2	6		ENSP00000374867.2		A0A0B4J1U4

Frequencies

GnomAD3 genomes

AF:

0.000402

AC:

AN:

136896

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000799

Gnomad AMI

AF:

0.00118

Gnomad AMR

AF:

0.00132

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:

0.000485

Gnomad OTH

AF:

0.00157

GnomAD3 exomes

AF:

0.000400

AC:

AN:

220058

Hom.:

AF XY:

0.000472

AC XY:

AN XY:

120706

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000323

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000668

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000716

Gnomad OTH exome

AF:

0.000540

GnomAD4 exome

AF:

0.000458

AC:

264

AN:

576582

Hom.:

Cov.:

AF XY:

0.000538

AC XY:

170

AN XY:

315934

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000504

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000585

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000630

Gnomad4 OTH exome

AF:

0.000740

GnomAD4 genome

AF:

0.000401

AC:

AN:

137006

Hom.:

Cov.:

AF XY:

0.000422

AC XY:

AN XY:

66382

show subpopulations

Gnomad4 AFR

AF:

0.0000797

Gnomad4 AMR

AF:

0.00132

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000485

Gnomad4 OTH

AF:

0.00155

Alfa

AF:

0.000480

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

Dec 01, 2022

TRG-AS1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.5

DANN

Benign

0.89

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

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