rs1491748

Variant names:

• chr3-68338842-G-A
• rs1491748
• NM_213609.4:c.119-78438G>A

Variant summary

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

The NM_213609.4(TAFA1):​c.119-78438G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,050 control chromosomes in the GnomAD database, including 9,526 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 0.34 (9526 hom., cov: 32)
• Consequence: TAFA1 NM_213609.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA1	NM_213609.4	c.119-78438G>A		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.119-78438G>A		intron_variant	Intron 2 of 4	1	NM_213609.4	ENSP00000418575.1
TAFA1	ENST00000496687.1	c.119-78438G>A		intron_variant	Intron 1 of 3	1		ENSP00000417496.1
TAFA1	ENST00000491017.1	n.507-78438G>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51888 AN: 151932 Hom.: 9525 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.341 AC: 51910 AN: 152050 Hom.: 9526 Cov.: 32 AF XY: 0.345 AC XY: 25660 AN XY: 74334

African (AFR) AF: 0.219 AC: 9066 AN: 41480

American (AMR) AF: 0.412 AC: 6304 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1319 AN: 3466

East Asian (EAS) AF: 0.458 AC: 2364 AN: 5166

South Asian (SAS) AF: 0.508 AC: 2447 AN: 4820

European-Finnish (FIN) AF: 0.349 AC: 3686 AN: 10570

Middle Eastern (MID) AF: 0.369 AC: 107 AN: 290

European-Non Finnish (NFE) AF: 0.374 AC: 25408 AN: 67950

Other (OTH) AF: 0.377 AC: 797 AN: 2112

Alfa AF: 0.371 Hom.: 34790

Bravo AF: 0.342

Asia WGS AF: 0.450 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.63
PhyloP100		0.56
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: rs1491748; hg19: chr3-68387992;