7-142727107-T-C

Position:

• chr7-142727107-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663830.1(ENSG00000286831):​n.659A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,718 control chromosomes in the GnomAD database, including 16,088 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 0.43 (16088 hom., cov: 29)
• Consequence: ENSG00000286831 ENST00000663830.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

Genes affected

ENSG00000286831 (HGNC:):

TRB (HGNC:12155):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRB		n.142727107T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286831	ENST00000663830.1	n.659A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65372 AN: 151600 Hom.: 16087 Cov.: 29

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.431 AC: 65386 AN: 151718 Hom.: 16088 Cov.: 29 AF XY: 0.429 AC XY: 31839 AN XY: 74134

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.462

Alfa AF: 0.529 Hom.: 36936

Bravo AF: 0.421

Asia WGS AF: 0.238 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6959895; hg19: chr7-142434960;