chr12-62229316-A-C

Variant names:

• chr12-62229316-A-C
• rs7313479
• ENST00000549379.5:n.-212+29447T>G

Variant summary

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

The ENST00000549379.5(TAFA2):​n.-212+29447T>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 2 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=-0.88).
• 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 rank	MANE	Protein	UniProt
TAFA2	XM_024448962.2	c.146+29447T>G		intron_variant	Intron 2 of 5		XP_024304730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA2	ENST00000549379.5	n.-212+29447T>G		intron_variant	Intron 2 of 8	1		ENSP00000447584.1
TAFA2	ENST00000551619.5	c.-130+29447T>G		intron_variant	Intron 1 of 5	2		ENSP00000447305.1
TAFA2	ENST00000552075.5	c.2+29447T>G		intron_variant	Intron 2 of 4	4		ENSP00000449516.1

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

African (AFR) AF: 0.273 AC: 11316 AN: 41388

American (AMR) AF: 0.243 AC: 3715 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3472

East Asian (EAS) AF: 0.346 AC: 1789 AN: 5174

South Asian (SAS) AF: 0.449 AC: 2165 AN: 4820

European-Finnish (FIN) AF: 0.498 AC: 5243 AN: 10538

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27389 AN: 67852

Other (OTH) AF: 0.370 AC: 779 AN: 2108

Alfa AF: 0.400 Hom.: 5454

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
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7313479; hg19: chr12-62623097;