12-62217079-A-G

Variant names:

• chr12-62217079-A-G
• rs11615916
• ENST00000549379.5:n.-212+41684T>C

Variant summary

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

The ENST00000549379.5(TAFA2):​n.-212+41684T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,234 control chromosomes in the GnomAD database, including 1,000 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 0.11 (1000 hom., cov: 32)
• Consequence: TAFA2 ENST00000549379.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA2	XM_024448962.2	c.146+41684T>C		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+41684T>C		intron_variant	Intron 2 of 8	1		ENSP00000447584.1
TAFA2	ENST00000551619.5	c.-130+41684T>C		intron_variant	Intron 1 of 5	2		ENSP00000447305.1
TAFA2	ENST00000552075.5	c.2+41684T>C		intron_variant	Intron 2 of 4	4		ENSP00000449516.1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16319 AN: 152116 Hom.: 999 Cov.: 32

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.107 AC: 16318 AN: 152234 Hom.: 1000 Cov.: 32 AF XY: 0.107 AC XY: 8000 AN XY: 74428

African (AFR) AF: 0.0676 AC: 2810 AN: 41544

American (AMR) AF: 0.120 AC: 1838 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3470

East Asian (EAS) AF: 0.0258 AC: 134 AN: 5186

South Asian (SAS) AF: 0.126 AC: 608 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1180 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8791 AN: 68000

Other (OTH) AF: 0.117 AC: 247 AN: 2114

Alfa AF: 0.122 Hom.: 3413

Bravo AF: 0.106

Asia WGS AF: 0.0790 AC: 278 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	8.6
DANN	Benign	0.72
PhyloP100		1.8
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: rs11615916; hg19: chr12-62610860;