NM_213609.4:c.119-55311T>G

Variant names:

• chr3-68361969-T-G
• rs17047573
• NM_213609.4:c.119-55311T>G

Variant summary

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

The NM_213609.4(TAFA1):​c.119-55311T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,128 control chromosomes in the GnomAD database, including 484 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 0.055 (484 hom., cov: 32)
• Consequence: TAFA1 NM_213609.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 4 publications found

Genes affected

TAFA1 (HGNC:21587): (TAFA chemokine like family member 1) 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_213609.4. 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
	TAFA1	NM_213609.4	MANE Select	c.119-55311T>G		intron	N/A	NP_998774.2
	TAFA1	NM_001252216.2		c.119-55311T>G		intron	N/A	NP_001239145.1
	TAFA1	NM_001438030.1		c.119-55311T>G		intron	N/A	NP_001424959.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA1	ENST00000478136.6	TSL:1 MANE Select	c.119-55311T>G		intron	N/A	ENSP00000418575.1
	TAFA1	ENST00000496687.1	TSL:1	c.119-55311T>G		intron	N/A	ENSP00000417496.1
	TAFA1	ENST00000491017.1	TSL:5	n.507-55311T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8303 AN: 152010 Hom.: 479 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00907

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0547 AC: 8323 AN: 152128 Hom.: 484 Cov.: 32 AF XY: 0.0581 AC XY: 4321 AN XY: 74366

African (AFR) AF: 0.132 AC: 5484 AN: 41506

American (AMR) AF: 0.0226 AC: 345 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.166 AC: 854 AN: 5154

South Asian (SAS) AF: 0.112 AC: 542 AN: 4820

European-Finnish (FIN) AF: 0.0359 AC: 381 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00906 AC: 616 AN: 67982

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.0236 Hom.: 610

Bravo AF: 0.0540

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		-0.094
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: rs17047573; hg19: chr3-68411119;