NM_178539.5:c.107-49670A>G

Variant names:

• chr12-61804694-T-C
• rs7304109
• NM_178539.5:c.107-49670A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178539.5(TAFA2):​c.107-49670A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,808 control chromosomes in the GnomAD database, including 9,057 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 0.34 (9057 hom., cov: 32)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743
• Publications: 3 publications found

Genes affected

TAFA2 (HGNC:21589): (TAFA chemokine like family member 2) 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. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA2	NM_178539.5	c.107-49670A>G		intron_variant	Intron 2 of 4	ENST00000416284.8	NP_848634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA2	ENST00000416284.8	c.107-49670A>G		intron_variant	Intron 2 of 4	1	NM_178539.5	ENSP00000393987.3

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51546 AN: 151692 Hom.: 9053 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.340 AC: 51559 AN: 151808 Hom.: 9057 Cov.: 32 AF XY: 0.339 AC XY: 25129 AN XY: 74180

African (AFR) AF: 0.246 AC: 10184 AN: 41466

American (AMR) AF: 0.301 AC: 4601 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3466

East Asian (EAS) AF: 0.389 AC: 2005 AN: 5160

South Asian (SAS) AF: 0.351 AC: 1690 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4240 AN: 10542

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26515 AN: 67778

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.368 Hom.: 32485

Bravo AF: 0.327

Asia WGS AF: 0.359 AC: 1247 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.78
PhyloP100		0.74
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7304109; hg19: chr12-62198475;