chr12-62164533-C-T

Variant names:

• chr12-62164533-C-T
• rs10784285
• NM_178539.5:c.-2+26726G>A

Variant summary

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

The NM_178539.5(TAFA2):​c.-2+26726G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,936 control chromosomes in the GnomAD database, including 22,376 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 0.54 (22376 hom., cov: 32)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178539.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA2	NM_178539.5	MANE Select	c.-2+26726G>A		intron	N/A	NP_848634.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA2	ENST00000416284.8	TSL:1 MANE Select	c.-2+26726G>A		intron	N/A	ENSP00000393987.3
	TAFA2	ENST00000549379.5	TSL:1	n.-212+94230G>A		intron	N/A	ENSP00000447584.1
	TAFA2	ENST00000551619.5	TSL:2	c.-130+94230G>A		intron	N/A	ENSP00000447305.1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81740 AN: 151816 Hom.: 22379 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.538 AC: 81764 AN: 151936 Hom.: 22376 Cov.: 32 AF XY: 0.537 AC XY: 39911 AN XY: 74264

African (AFR) AF: 0.477 AC: 19762 AN: 41438

American (AMR) AF: 0.587 AC: 8953 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2345 AN: 3468

East Asian (EAS) AF: 0.635 AC: 3286 AN: 5174

South Asian (SAS) AF: 0.519 AC: 2503 AN: 4820

European-Finnish (FIN) AF: 0.515 AC: 5443 AN: 10566

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37417 AN: 67904

Other (OTH) AF: 0.565 AC: 1195 AN: 2114

Alfa AF: 0.556 Hom.: 43072

Bravo AF: 0.547

Asia WGS AF: 0.509 AC: 1771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.74
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10784285; hg19: chr12-62558314;