12-61877602-C-T

Variant names:

• chr12-61877602-C-T
• rs10877756
• NM_178539.5:c.-1-10176G>A

Variant summary

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

The ENST00000416284.8(TAFA2):​c.-1-10176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,976 control chromosomes in the GnomAD database, including 12,664 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 0.39 (12664 hom., cov: 31)
• Consequence: TAFA2 ENST00000416284.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416284.8. 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.-1-10176G>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.-1-10176G>A		intron	N/A	ENSP00000393987.3
	TAFA2	ENST00000549379.5	TSL:1	n.-1-10176G>A		intron	N/A	ENSP00000447584.1
	TAFA2	ENST00000551619.5	TSL:2	c.-1-10176G>A		intron	N/A	ENSP00000447305.1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59493 AN: 151856 Hom.: 12662 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.392 AC: 59506 AN: 151976 Hom.: 12664 Cov.: 31 AF XY: 0.393 AC XY: 29213 AN XY: 74286

African (AFR) AF: 0.217 AC: 8996 AN: 41446

American (AMR) AF: 0.436 AC: 6659 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1305 AN: 3466

East Asian (EAS) AF: 0.346 AC: 1785 AN: 5160

South Asian (SAS) AF: 0.433 AC: 2086 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5145 AN: 10552

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32104 AN: 67936

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.435 Hom.: 46020

Bravo AF: 0.383

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.37
DANN	Benign	0.29
PhyloP100		-0.89
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: rs10877756; hg19: chr12-62271383;