7-142307367-AGTGTGTGTGTGTGTGTGT-AGT

Variant names:

• chr7-142307367-AGTGTGTGTGTGTGTGT-A
• rs3222967

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.020 (54 hom., cov: 0)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 1 publications found

Genes affected

TRB (HGNC:12155):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0196 (2873/146322) while in subpopulation NFE AF = 0.031 (2055/66374). AF 95% confidence interval is 0.0298. There are 54 homozygotes in GnomAd4. There are 1397 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 54 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142307385_142307400delTGTGTGTGTGTGTGTG		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0196 AC: 2873 AN: 146216 Hom.: 54 Cov.: 0

Gnomad AFR AF: 0.00553

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.0129

Gnomad ASJ AF: 0.0152

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0171

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

GnomAD4 genome AF: 0.0196 AC: 2873 AN: 146322 Hom.: 54 Cov.: 0 AF XY: 0.0197 AC XY: 1397 AN XY: 71052

African (AFR) AF: 0.00552 AC: 219 AN: 39686

American (AMR) AF: 0.0129 AC: 189 AN: 14694

Ashkenazi Jewish (ASJ) AF: 0.0152 AC: 52 AN: 3424

East Asian (EAS) AF: 0.00 AC: 0 AN: 4900

South Asian (SAS) AF: 0.00602 AC: 27 AN: 4486

European-Finnish (FIN) AF: 0.0310 AC: 296 AN: 9560

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.0310 AC: 2055 AN: 66374

Other (OTH) AF: 0.0169 AC: 34 AN: 2008

Alfa AF: 0.0622 Hom.: 1268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs3222967; hg19: chr7-142007188;