chr7-142749077-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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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 v4.9

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;