NM_213609.4:c.119-53556A>G

Variant names:

• chr3-68363724-A-G
• rs17047586
• NM_213609.4:c.119-53556A>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.119-53556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 152,316 control chromosomes in the GnomAD database, including 86 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 0.011 (86 hom., cov: 33)
• Consequence: TAFA1 NM_213609.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA1	NM_213609.4	c.119-53556A>G		intron_variant	Intron 2 of 4	ENST00000478136.6	NP_998774.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA1	ENST00000478136.6	c.119-53556A>G		intron_variant	Intron 2 of 4	1	NM_213609.4	ENSP00000418575.1
TAFA1	ENST00000496687.1	c.119-53556A>G		intron_variant	Intron 1 of 3	1		ENSP00000417496.1
TAFA1	ENST00000491017.1	n.507-53556A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0108 AC: 1641 AN: 152198 Hom.: 86 Cov.: 33

Gnomad AFR AF: 0.00135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00334

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0323

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00135

Gnomad OTH AF: 0.00813

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

GnomAD4 genome AF: 0.0108 AC: 1641 AN: 152316 Hom.: 86 Cov.: 33 AF XY: 0.0138 AC XY: 1026 AN XY: 74476

African (AFR) AF: 0.00137 AC: 57 AN: 41584

American (AMR) AF: 0.00334 AC: 51 AN: 15290

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

East Asian (EAS) AF: 0.161 AC: 832 AN: 5168

South Asian (SAS) AF: 0.0498 AC: 240 AN: 4822

European-Finnish (FIN) AF: 0.0323 AC: 343 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00135 AC: 92 AN: 68038

Other (OTH) AF: 0.00993 AC: 21 AN: 2114

Alfa AF: 0.00607 Hom.: 9

Bravo AF: 0.00782

Asia WGS AF: 0.0950 AC: 330 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.59
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: rs17047586; hg19: chr3-68412874;