NM_213609.4:c.119-138052C>T

Variant names:

• chr3-68279228-C-T
• rs4428185
• NM_213609.4:c.119-138052C>T

Variant summary

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

The NM_213609.4(TAFA1):​c.119-138052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,044 control chromosomes in the GnomAD database, including 42,170 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 0.74 (42170 hom., cov: 32)
• Consequence: TAFA1 NM_213609.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 2 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]

LOC107986019 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.882 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.119-138052C>T		intron	N/A	NP_998774.2
	TAFA1	NM_001252216.2		c.119-138052C>T		intron	N/A	NP_001239145.1
	TAFA1	NM_001438030.1		c.119-138052C>T		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.119-138052C>T		intron	N/A	ENSP00000418575.1
	TAFA1	ENST00000496687.1	TSL:1	c.119-138052C>T		intron	N/A	ENSP00000417496.1
	TAFA1	ENST00000491017.1	TSL:5	n.506+28317C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112437 AN: 151926 Hom.: 42123 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.740 AC: 112543 AN: 152044 Hom.: 42170 Cov.: 32 AF XY: 0.742 AC XY: 55129 AN XY: 74306

African (AFR) AF: 0.832 AC: 34535 AN: 41490

American (AMR) AF: 0.674 AC: 10287 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2477 AN: 3472

East Asian (EAS) AF: 0.903 AC: 4676 AN: 5178

South Asian (SAS) AF: 0.904 AC: 4360 AN: 4822

European-Finnish (FIN) AF: 0.703 AC: 7411 AN: 10542

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46381 AN: 67964

Other (OTH) AF: 0.758 AC: 1602 AN: 2114

Alfa AF: 0.702 Hom.: 62442

Bravo AF: 0.743

Asia WGS AF: 0.889 AC: 3090 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.67
PhyloP100		-0.22
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: rs4428185; hg19: chr3-68328378;