rs78492

Variant names:

• chr22-48781165-C-T
• rs78492
• ENST00000336769.9:c.391-69593C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000336769.9(TAFA5):​c.391-69593C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,178 control chromosomes in the GnomAD database, including 64,504 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 0.92 (64504 hom., cov: 31)
• Consequence: TAFA5 ENST00000336769.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 0 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=-1.2).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.935 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA5	ENST00000336769.9	TSL:4	c.391-69593C>T		intron	N/A	ENSP00000336812.5

Frequencies

GnomAD3 genomes AF: 0.921 AC: 139978 AN: 152060 Hom.: 64455 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.921 AC: 140085 AN: 152178 Hom.: 64504 Cov.: 31 AF XY: 0.922 AC XY: 68593 AN XY: 74390

African (AFR) AF: 0.917 AC: 38071 AN: 41532

American (AMR) AF: 0.927 AC: 14176 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3142 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4470 AN: 5130

South Asian (SAS) AF: 0.958 AC: 4623 AN: 4824

European-Finnish (FIN) AF: 0.940 AC: 9972 AN: 10604

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.921 AC: 62618 AN: 68014

Other (OTH) AF: 0.903 AC: 1907 AN: 2112

Alfa AF: 0.919 Hom.: 133501

Bravo AF: 0.917

Asia WGS AF: 0.917 AC: 3190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.060
DANN	Benign	0.66
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs78492; hg19: chr22-49176977;