7-142490201-C-T

Variant names:

• chr7-142490201-C-T
• rs11982969

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0167 in 120,722 control chromosomes in the GnomAD database, including 47 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 0.017 (47 hom., cov: 31)
• Consequence: TRB intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 2 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=-0.93).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0167 (2014/120722) while in subpopulation AFR AF = 0.0506 (1909/37720). AF 95% confidence interval is 0.0487. There are 47 homozygotes in GnomAd4. There are 907 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRB		n.142490201C>T		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0167 AC: 2014 AN: 120604 Hom.: 47 Cov.: 31

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00606

Gnomad ASJ AF: 0.00118

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000576

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00394

Gnomad NFE AF: 0.0000954

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0167 AC: 2014 AN: 120722 Hom.: 47 Cov.: 31 AF XY: 0.0155 AC XY: 907 AN XY: 58666

African (AFR) AF: 0.0506 AC: 1909 AN: 37720

American (AMR) AF: 0.00605 AC: 69 AN: 11404

Ashkenazi Jewish (ASJ) AF: 0.00118 AC: 3 AN: 2532

East Asian (EAS) AF: 0.00 AC: 0 AN: 2430

South Asian (SAS) AF: 0.000288 AC: 1 AN: 3468

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8084

Middle Eastern (MID) AF: 0.00420 AC: 1 AN: 238

European-Non Finnish (NFE) AF: 0.0000954 AC: 5 AN: 52426

Other (OTH) AF: 0.0160 AC: 26 AN: 1620

Alfa AF: 0.00710 Hom.: 1

Bravo AF: 0.0146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs11982969; hg19: chr7-142141746;