rs80515

Variant names:

• chr22-48782499-A-G
• rs80515
• ENST00000336769.9:c.391-68259A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000336769.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA5	ENST00000336769.9	TSL:4	c.391-68259A>G		intron	N/A	ENSP00000336812.5	B1B1J6

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

African (AFR) AF: 0.651 AC: 26995 AN: 41472

American (AMR) AF: 0.866 AC: 13245 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2971 AN: 3468

East Asian (EAS) AF: 0.843 AC: 4333 AN: 5138

South Asian (SAS) AF: 0.928 AC: 4471 AN: 4818

European-Finnish (FIN) AF: 0.902 AC: 9570 AN: 10608

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60766 AN: 68014

Other (OTH) AF: 0.820 AC: 1734 AN: 2114

Alfa AF: 0.873 Hom.: 32328

Bravo AF: 0.809

Asia WGS AF: 0.870 AC: 3025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.18
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs80515; hg19: chr22-49178311;