12-61833395-C-T

Variant names:

• chr12-61833395-C-T
• rs7977950
• NM_178539.5:c.106+33925G>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.106+33925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 151,808 control chromosomes in the GnomAD database, including 58,983 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 0.88 (58983 hom., cov: 30)
• Consequence: TAFA2 NM_178539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA2	NM_178539.5	c.106+33925G>A		intron_variant	Intron 2 of 4	ENST00000416284.8	NP_848634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA2	ENST00000416284.8	c.106+33925G>A		intron_variant	Intron 2 of 4	1	NM_178539.5	ENSP00000393987.3

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133538 AN: 151690 Hom.: 58918 Cov.: 30

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.880 AC: 133658 AN: 151808 Hom.: 58983 Cov.: 30 AF XY: 0.879 AC XY: 65169 AN XY: 74144

African (AFR) AF: 0.947 AC: 39256 AN: 41448

American (AMR) AF: 0.874 AC: 13278 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2755 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4522 AN: 5116

South Asian (SAS) AF: 0.881 AC: 4255 AN: 4830

European-Finnish (FIN) AF: 0.849 AC: 8935 AN: 10530

Middle Eastern (MID) AF: 0.776 AC: 225 AN: 290

European-Non Finnish (NFE) AF: 0.852 AC: 57871 AN: 67926

Other (OTH) AF: 0.845 AC: 1774 AN: 2100

Alfa AF: 0.877 Hom.: 9501

Bravo AF: 0.884

Asia WGS AF: 0.873 AC: 3032 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.24
PhyloP100		-0.76
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: rs7977950; hg19: chr12-62227176;