Variant 3-68733148-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_182522.5(TAFA4):c.417G>A(p.Thr139=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00207 in 1,613,184 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0016 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0021 ( 8 hom. )

Consequence

TAFA4
NM_182522.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.29

Variant links:

Genes affected

TAFA4 (HGNC:21591): (TAFA chemokine like family member 4) This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small secreted proteins. These proteins contain conserved cysteine residues at fixed positions, and are distantly related to MIP-1alpha, a member of the CC-chemokine family. The TAFA proteins are predominantly expressed in specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines, that act as regulators of immune and nervous cells. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011]

TAFA4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 3-68733148-C-T is Benign according to our data. Variant chr3-68733148-C-T is described in ClinVar as [Benign]. Clinvar id is 719249.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.29 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TAFA4	NM_182522.5 linkuse as main transcript	c.417G>A	p.Thr139=	synonymous_variant	6/6	ENST00000295569.12
TAFA4	XM_011533371.2 linkuse as main transcript	c.376G>A	p.Ala126Thr	missense_variant	6/6
TAFA4	XM_011533372.2 linkuse as main transcript	c.376G>A	p.Ala126Thr	missense_variant	6/6
TAFA4	NM_001005527.3 linkuse as main transcript	c.417G>A	p.Thr139=	synonymous_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA4	ENST00000295569.12 linkuse as main transcript	c.417G>A	p.Thr139=	synonymous_variant	6/6	1	NM_182522.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00160

AC:

243

AN:

152112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000796

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00256

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00436

Gnomad FIN

AF:

0.000660

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00209

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00170

AC:

427

AN:

250698

Hom.:

AF XY:

0.00185

AC XY:

251

AN XY:

135560

show subpopulations

Gnomad AFR exome

AF:

0.000616

Gnomad AMR exome

AF:

0.000724

Gnomad ASJ exome

AF:

0.0000994

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00421

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00214

Gnomad OTH exome

AF:

0.00229

GnomAD4 exome

AF:

0.00212

AC:

3095

AN:

1460954

Hom.:

Cov.:

AF XY:

0.00218

AC XY:

1587

AN XY:

726772

show subpopulations

Gnomad4 AFR exome

AF:

0.000449

Gnomad4 AMR exome

AF:

0.000918

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00382

Gnomad4 FIN exome

AF:

0.000412

Gnomad4 NFE exome

AF:

0.00227

Gnomad4 OTH exome

AF:

0.00200

GnomAD4 genome

AF:

0.00160

AC:

243

AN:

152230

Hom.:

Cov.:

AF XY:

0.00160

AC XY:

119

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00436

Gnomad4 FIN

AF:

0.000660

Gnomad4 NFE

AF:

0.00209

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00186

Hom.:

Bravo

AF:

0.00138

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00252

EpiControl

AF:

0.00173

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

0.79

DANN

Benign

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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