chr7-142749281-A-C

Position:

• chr7-142749281-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.555 in 145,756 control chromosomes in the GnomAD database, including 21,910 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.56 (21910 hom., cov: 29)
• Consequence: TRB intragenic
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.05

Genes affected

TRB (HGNC:12155):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 7-142749281-A-C is Benign according to our data. Variant chr7-142749281-A-C is described in ClinVar as [Benign]. Clinvar id is 1169050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRB		n.142749281A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.555 AC: 80858 AN: 145652 Hom.: 21898 Cov.: 29

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.441

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.555 AC: 80911 AN: 145756 Hom.: 21910 Cov.: 29 AF XY: 0.550 AC XY: 39201 AN XY: 71286

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.547

Alfa AF: 0.437 Hom.: 1011

Asia WGS AF: 0.275 AC: 962 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary pancreatitis Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 06, 2023

- -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.022
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4726576; hg19: chr7-142457132; COSMIC: COSV61195680;