NM_178539.5:c.-2+137116A>G

Variant names:

• chr12-62054143-T-C
• rs348633
• NM_178539.5:c.-2+137116A>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.-2+137116A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,124 control chromosomes in the GnomAD database, including 52,069 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 0.83 (52069 hom., cov: 31)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA2	NM_178539.5	c.-2+137116A>G		intron_variant	Intron 1 of 4	ENST00000416284.8	NP_848634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA2	ENST00000416284.8	c.-2+137116A>G		intron_variant	Intron 1 of 4	1	NM_178539.5	ENSP00000393987.3

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125509 AN: 152008 Hom.: 52003 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.826 AC: 125632 AN: 152124 Hom.: 52069 Cov.: 31 AF XY: 0.826 AC XY: 61453 AN XY: 74356

African (AFR) AF: 0.830 AC: 34428 AN: 41494

American (AMR) AF: 0.828 AC: 12651 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2483 AN: 3472

East Asian (EAS) AF: 0.666 AC: 3430 AN: 5154

South Asian (SAS) AF: 0.731 AC: 3515 AN: 4810

European-Finnish (FIN) AF: 0.871 AC: 9219 AN: 10588

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57081 AN: 68014

Other (OTH) AF: 0.820 AC: 1731 AN: 2112

Alfa AF: 0.827 Hom.: 6348

Bravo AF: 0.822

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.72
DANN	Benign	0.69
PhyloP100		-0.92
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: rs348633; hg19: chr12-62447924;