rs16999684

chr22-48671066-A-C

Variant summary

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

The NM_001082967.3(TAFA5):c.262+24320A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,092 control chromosomes in the GnomAD database, including 9,954 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 0.33 (9954 hom., cov: 33)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAFA5	NM_001082967.3	c.262+24320A>C		intron_variant		ENST00000402357.6
TAFA5	NM_015381.7	c.241+24320A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA5	ENST00000402357.6	c.262+24320A>C		intron_variant		1	NM_001082967.3	P4
TAFA5	ENST00000336769.9	c.262+24320A>C		intron_variant		4
TAFA5	ENST00000358295.9	c.241+24320A>C		intron_variant		2		A1
TAFA5	ENST00000473898.1	n.120-36651A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49474 AN: 151974 Hom.: 9933 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.326 AC: 49547 AN: 152092 Hom.: 9954 Cov.: 33 AF XY: 0.322 AC XY: 23968 AN XY: 74372

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.305

Alfa AF: 0.270 Hom.: 2483

Bravo AF: 0.334

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	7.0
Dann	Benign	0.68

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: rs16999684; hg19: chr22-49066878;