7-38367276-T-C

Variant names:

• chr7-38367276-T-C
• rs10240848

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.332 in 152,022 control chromosomes in the GnomAD database, including 8,646 homozygotes. 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 0.33 (8646 hom., cov: 31)
• Consequence: TRG intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 7 publications found

Genes affected

TRG (HGNC:12271):

TRG-AS1 (HGNC:48974): (T cell receptor gamma locus antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRG-AS1	NR_040085.2		n.592-8281T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRG-AS1	ENST00000629357.1	TSL:2	n.398-8281T>C		intron	N/A
	TRG-AS1	ENST00000661780.1		n.265-8281T>C		intron	N/A
	TRG-AS1	ENST00000669822.2		n.446-6089T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50443 AN: 151904 Hom.: 8641 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.305

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.332 AC: 50486 AN: 152022 Hom.: 8646 Cov.: 31 AF XY: 0.333 AC XY: 24716 AN XY: 74312

African (AFR) AF: 0.392 AC: 16261 AN: 41440

American (AMR) AF: 0.295 AC: 4512 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3472

East Asian (EAS) AF: 0.306 AC: 1583 AN: 5166

South Asian (SAS) AF: 0.195 AC: 941 AN: 4820

European-Finnish (FIN) AF: 0.381 AC: 4029 AN: 10580

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21187 AN: 67950

Other (OTH) AF: 0.303 AC: 637 AN: 2104

Alfa AF: 0.318 Hom.: 1904

Bravo AF: 0.334

Asia WGS AF: 0.245 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.41
PhyloP100		0.095

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10240848; hg19: chr7-38406877;