rs80515

Positions:

• chr22-48782499-A-G

Variant summary

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

The ENST00000336769.9(TAFA5):​c.391-68259A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,126 control chromosomes in the GnomAD database, including 52,318 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 0.82 (52318 hom., cov: 32)
• Consequence: TAFA5 ENST00000336769.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 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.391-68259A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125058 AN: 152008 Hom.: 52300 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.822 AC: 125122 AN: 152126 Hom.: 52318 Cov.: 32 AF XY: 0.827 AC XY: 61516 AN XY: 74364

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.820

Alfa AF: 0.874 Hom.: 29171

Bravo AF: 0.809

Asia WGS AF: 0.870 AC: 3025 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	0.016
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs80515; hg19: chr22-49178311;