Variant chr3-196052101-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001128148.3(TFRC):c.2124G>A(p.Thr708=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,613,898 control chromosomes in the GnomAD database, including 9,214 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.076 ( 568 hom., cov: 32)

Exomes 𝑓: 0.10 ( 8646 hom. )

Consequence

TFRC
NM_001128148.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.599

Variant links:

Genes affected

TFRC (HGNC:11763): (transferrin receptor) This gene encodes a cell surface receptor necessary for cellular iron uptake by the process of receptor-mediated endocytosis. This receptor is required for erythropoiesis and neurologic development. Multiple alternatively spliced variants have been identified. [provided by RefSeq, Sep 2015]

TFRC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 3-196052101-C-T is Benign according to our data. Variant chr3-196052101-C-T is described in ClinVar as [Benign]. Clinvar id is 1166123.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.599 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TFRC	NM_001128148.3 linkuse as main transcript	c.2124G>A	p.Thr708=	synonymous_variant	19/19	ENST00000360110.9	NP_001121620.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TFRC	ENST00000360110.9 linkuse as main transcript	c.2124G>A	p.Thr708=	synonymous_variant	19/19	1	NM_001128148.3	ENSP00000353224	P2

Frequencies

GnomAD3 genomes

AF:

0.0759

AC:

11531

AN:

151962

Hom.:

565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0184

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0644

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.0871

GnomAD3 exomes

AF:

0.0898

AC:

22574

AN:

251330

Hom.:

1244

AF XY:

0.0935

AC XY:

12707

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.0160

Gnomad AMR exome

AF:

0.0631

Gnomad ASJ exome

AF:

0.104

Gnomad EAS exome

AF:

0.00228

Gnomad SAS exome

AF:

0.121

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.109

Gnomad OTH exome

AF:

0.0966

GnomAD4 exome

AF:

0.104

AC:

152730

AN:

1461818

Hom.:

8646

Cov.:

AF XY:

0.106

AC XY:

77152

AN XY:

727204

show subpopulations

Gnomad4 AFR exome

AF:

0.0155

Gnomad4 AMR exome

AF:

0.0632

Gnomad4 ASJ exome

AF:

0.0993

Gnomad4 EAS exome

AF:

0.00171

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.108

Gnomad4 NFE exome

AF:

0.111

Gnomad4 OTH exome

AF:

0.100

GnomAD4 genome

AF:

0.0759

AC:

11539

AN:

152080

Hom.:

568

Cov.:

AF XY:

0.0748

AC XY:

5561

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.0183

Gnomad4 AMR

AF:

0.0646

Gnomad4 ASJ

AF:

0.101

Gnomad4 EAS

AF:

0.00270

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.109

Gnomad4 OTH

AF:

0.0862

Alfa

AF:

0.0973

Hom.:

405

Bravo

AF:

0.0683

Asia WGS

AF:

0.0530

AC:

183

AN:

3478

EpiCase

AF:

0.110

EpiControl

AF:

0.104

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

0.68

DANN

Benign

0.48

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over