rs7313479

chr12-62229316-A-Cchr12-62229316-A-G

Variant summary

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

The ENST00000549379.5(TAFA2):c.-212+29447T>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,834 control chromosomes in the GnomAD database, including 10,135 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 0.36 (10135 hom., cov: 32)
• Consequence: TAFA2 ENST00000549379.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAFA2	XM_024448962.2	c.146+29447T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA2	ENST00000549379.5	c.-212+29447T>G		intron_variant, NMD_transcript_variant		1
TAFA2	ENST00000551619.5	c.-130+29447T>G		intron_variant		2		P1
TAFA2	ENST00000552075.5	c.2+29447T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54105 AN: 151716 Hom.: 10118 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.357 AC: 54149 AN: 151834 Hom.: 10135 Cov.: 32 AF XY: 0.358 AC XY: 26601 AN XY: 74226

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.370

Alfa AF: 0.401 Hom.: 4790

Bravo AF: 0.329

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.1
Dann	Benign	0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7313479; hg19: chr12-62623097;