12-62029982-T-G

Position:

• chr12-62029982-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178539.5(TAFA2):​c.-2+161277A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,032 control chromosomes in the GnomAD database, including 49,004 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 0.80 (49004 hom., cov: 31)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

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=-0.89).
• 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/exons	MANE	Protein	UniProt
TAFA2	NM_178539.5	c.-2+161277A>C		intron_variant		ENST00000416284.8	NP_848634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAFA2	ENST00000416284.8	c.-2+161277A>C		intron_variant		1	NM_178539.5	ENSP00000393987.3

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121552 AN: 151914 Hom.: 48944 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.800 AC: 121669 AN: 152032 Hom.: 49004 Cov.: 31 AF XY: 0.801 AC XY: 59576 AN XY: 74336

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.798

Alfa AF: 0.818 Hom.: 32179

Bravo AF: 0.793

Asia WGS AF: 0.727 AC: 2528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.71

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: rs348691; hg19: chr12-62423763;