rs9847748

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_182522.5(TAFA4):​c.-122-11227T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,118 control chromosomes in the GnomAD database, including 17,375 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 0.46 ( 17375 hom., cov: 33)

Consequence

TAFA4
NM_182522.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TAFA4NM_182522.5 linkuse as main transcriptc.-122-11227T>C intron_variant ENST00000295569.12
TAFA4NM_001005527.3 linkuse as main transcriptc.-122-11227T>C intron_variant
TAFA4XM_011533371.2 linkuse as main transcriptc.-122-11227T>C intron_variant
TAFA4XM_011533372.2 linkuse as main transcriptc.-122-11227T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TAFA4ENST00000295569.12 linkuse as main transcriptc.-122-11227T>C intron_variant 1 NM_182522.5 P1
TAFA4ENST00000495737.1 linkuse as main transcriptc.-122-11227T>C intron_variant 4
TAFA4ENST00000634242.1 linkuse as main transcriptc.-122-11227T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.457
AC:
69493
AN:
152000
Hom.:
17341
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.596
Gnomad AMI
AF:
0.507
Gnomad AMR
AF:
0.546
Gnomad ASJ
AF:
0.233
Gnomad EAS
AF:
0.815
Gnomad SAS
AF:
0.489
Gnomad FIN
AF:
0.340
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.355
Gnomad OTH
AF:
0.412
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.457
AC:
69585
AN:
152118
Hom.:
17375
Cov.:
33
AF XY:
0.462
AC XY:
34324
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.596
Gnomad4 AMR
AF:
0.546
Gnomad4 ASJ
AF:
0.233
Gnomad4 EAS
AF:
0.815
Gnomad4 SAS
AF:
0.490
Gnomad4 FIN
AF:
0.340
Gnomad4 NFE
AF:
0.355
Gnomad4 OTH
AF:
0.419
Alfa
AF:
0.432
Hom.:
2244
Bravo
AF:
0.477
Asia WGS
AF:
0.651
AC:
2257
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.31
DANN
Benign
0.49

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.

Other links and lift over

dbSNP: rs9847748; hg19: chr3-68945688; API