12-61841052-C-T

Position:

• chr12-61841052-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAFA2	NM_178539.5	c.106+26268G>A		intron_variant		ENST00000416284.8	NP_848634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAFA2	ENST00000416284.8	c.106+26268G>A		intron_variant		1	NM_178539.5	ENSP00000393987.3

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

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.347

Alfa AF: 0.359 Hom.: 10097

Bravo AF: 0.322

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs2198776; hg19: chr12-62234833;