rs17605016

Positions:

• chr12-61856639-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.106+10681A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 152,020 control chromosomes in the GnomAD database, including 897 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 0.091 (897 hom., cov: 32)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

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 (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAFA2	NM_178539.5	c.106+10681A>C		intron_variant		ENST00000416284.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA2	ENST00000416284.8	c.106+10681A>C		intron_variant		1	NM_178539.5	P1

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13819 AN: 151902 Hom.: 895 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0782

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.0909 AC: 13823 AN: 152020 Hom.: 897 Cov.: 32 AF XY: 0.0931 AC XY: 6917 AN XY: 74294

Gnomad4 AFR AF: 0.0289

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0954

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.0965

Gnomad4 OTH AF: 0.0924

Alfa AF: 0.0886 Hom.: 78

Bravo AF: 0.0921

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.86

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: rs17605016; hg19: chr12-62250420;