rs1920101

Positions:

• chr12-62128857-G-A

Variant summary

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

The NM_178539.5(TAFA2):​c.-2+62402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,028 control chromosomes in the GnomAD database, including 3,117 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 0.20 (3117 hom., cov: 32)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

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]

TAFA2 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAFA2	NM_178539.5	c.-2+62402C>T		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+62402C>T		intron_variant		1	NM_178539.5	ENSP00000393987.3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29746 AN: 151910 Hom.: 3103 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.196 AC: 29793 AN: 152028 Hom.: 3117 Cov.: 32 AF XY: 0.202 AC XY: 15014 AN XY: 74320

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.197

Alfa AF: 0.174 Hom.: 501

Bravo AF: 0.204

Asia WGS AF: 0.234 AC: 815 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	1.1
DANN	Benign	0.48

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: rs1920101; hg19: chr12-62522638;