rs6008743

Positions:

• chr22-48503032-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001082967.3(TAFA5):​c.112+13328G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,154 control chromosomes in the GnomAD database, including 7,789 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 0.26 (7789 hom., cov: 33)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

TAFA5 (HGNC:21592): (TAFA chemokine like family member 5) 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, Sep 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAFA5	NM_001082967.3	c.112+13328G>A		intron_variant		ENST00000402357.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA5	ENST00000402357.6	c.112+13328G>A		intron_variant		1	NM_001082967.3	P4
TAFA5	ENST00000336769.9	c.112+13328G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38750 AN: 152036 Hom.: 7762 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.255 AC: 38826 AN: 152154 Hom.: 7789 Cov.: 33 AF XY: 0.247 AC XY: 18395 AN XY: 74386

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.0757

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.209

Alfa AF: 0.224 Hom.: 693

Bravo AF: 0.266

Asia WGS AF: 0.118 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6008743; hg19: chr22-48898844;