NM_178539.5:c.106+26268G>A

Variant names:

• chr12-61841052-C-T
• rs2198776
• NM_178539.5:c.106+26268G>A

Variant summary

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

The NM_178539.5(TAFA2):​c.106+26268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,742 control chromosomes in the GnomAD database, including 8,800 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 0.33 (8800 hom., cov: 31)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 9 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178539.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA2	NM_178539.5	MANE Select	c.106+26268G>A		intron	N/A	NP_848634.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA2	ENST00000416284.8	TSL:1 MANE Select	c.106+26268G>A		intron	N/A	ENSP00000393987.3
	TAFA2	ENST00000549379.5	TSL:1	n.106+26268G>A		intron	N/A	ENSP00000447584.1
	TAFA2	ENST00000551619.5	TSL:2	c.106+26268G>A		intron	N/A	ENSP00000447305.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50805 AN: 151624 Hom.: 8797 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.335 AC: 50817 AN: 151742 Hom.: 8800 Cov.: 31 AF XY: 0.335 AC XY: 24799 AN XY: 74136

African (AFR) AF: 0.255 AC: 10584 AN: 41436

American (AMR) AF: 0.294 AC: 4475 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1178 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1925 AN: 5088

South Asian (SAS) AF: 0.347 AC: 1666 AN: 4806

European-Finnish (FIN) AF: 0.398 AC: 4194 AN: 10534

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25685 AN: 67864

Other (OTH) AF: 0.347 AC: 733 AN: 2110

Alfa AF: 0.355 Hom.: 25642

Bravo AF: 0.322

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.60
PhyloP100		-0.027
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: rs2198776; hg19: chr12-62234833;