rs131026

Positions:

• chr22-48780096-G-A
• chr22-48780096-G-C
• chr22-48780096-G-T

Variant summary

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

The ENST00000336769.9(TAFA5):​c.391-70662G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,054 control chromosomes in the GnomAD database, including 20,722 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 0.46 (20722 hom., cov: 33)
• Consequence: TAFA5 ENST00000336769.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA5	ENST00000336769.9	c.391-70662G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69628 AN: 151936 Hom.: 20674 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.459 AC: 69733 AN: 152054 Hom.: 20722 Cov.: 33 AF XY: 0.460 AC XY: 34207 AN XY: 74322

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.435

Alfa AF: 0.297 Hom.: 9327

Bravo AF: 0.473

Asia WGS AF: 0.782 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs131026; hg19: chr22-49175908;