chr7-142727107-T-C

Variant names:

• chr7-142727107-T-C
• rs6959895
• ENST00000663830.1:n.659A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000286831 (HGNC:):

TRB (HGNC:12155):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663830.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286831	ENST00000663830.1		n.659A>G		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.204 AC: 8416 AN: 41350

American (AMR) AF: 0.530 AC: 8070 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1898 AN: 3466

East Asian (EAS) AF: 0.175 AC: 903 AN: 5174

South Asian (SAS) AF: 0.312 AC: 1497 AN: 4800

European-Finnish (FIN) AF: 0.544 AC: 5711 AN: 10504

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37342 AN: 67886

Other (OTH) AF: 0.462 AC: 973 AN: 2108

Alfa AF: 0.505 Hom.: 60149

Bravo AF: 0.421

Asia WGS AF: 0.238 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6959895;

hg19: chr7-142434960;