7-142749077-T-C

Variant names:

• chr7-142749077-T-C
• rs10273639

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 0.516 in 151,116 control chromosomes in the GnomAD database, including 20,792 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 0.52 (20792 hom., cov: 27)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 62 publications found

Genes affected

TRB (HGNC:12155):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142749077T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.516 AC: 77930 AN: 150998 Hom.: 20781 Cov.: 27

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.516 AC: 77981 AN: 151116 Hom.: 20792 Cov.: 27 AF XY: 0.512 AC XY: 37812 AN XY: 73830

African (AFR) AF: 0.434 AC: 17867 AN: 41146

American (AMR) AF: 0.570 AC: 8639 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1982 AN: 3458

East Asian (EAS) AF: 0.224 AC: 1153 AN: 5142

South Asian (SAS) AF: 0.305 AC: 1462 AN: 4794

European-Finnish (FIN) AF: 0.600 AC: 6254 AN: 10428

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 38943 AN: 67700

Other (OTH) AF: 0.523 AC: 1095 AN: 2092

Alfa AF: 0.555 Hom.: 84895

Bravo AF: 0.515

Asia WGS AF: 0.272 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.040
DANN	Benign	0.54
PhyloP100		-0.79
PromoterAI		0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10273639; hg19: chr7-142456928;