rs17047573

chr3-68361969-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAFA1	NM_213609.4	c.119-55311T>G		intron_variant		ENST00000478136.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA1	ENST00000478136.6	c.119-55311T>G		intron_variant		1	NM_213609.4	P1
TAFA1	ENST00000496687.1	c.119-55311T>G		intron_variant		1		P1
TAFA1	ENST00000491017.1	n.507-55311T>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0359

Gnomad4 NFE AF: 0.00906

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0172 Hom.: 186

Bravo AF: 0.0540

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.8
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs17047573; hg19: chr3-68411119;