rs133495

Variant names:

• chr22-48519759-G-A
• rs133495
• NM_001082967.3:c.112+30055G>A

Variant summary

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

The NM_001082967.3(TAFA5):​c.112+30055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 152,200 control chromosomes in the GnomAD database, including 406 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 0.060 (406 hom., cov: 33)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA5	NM_001082967.3	c.112+30055G>A		intron_variant	Intron 1 of 3	ENST00000402357.6	NP_001076436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA5	ENST00000402357.6	c.112+30055G>A		intron_variant	Intron 1 of 3	1	NM_001082967.3	ENSP00000383933.2
TAFA5	ENST00000336769.9	c.112+30055G>A		intron_variant	Intron 1 of 3	4		ENSP00000336812.5

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9174 AN: 152082 Hom.: 405 Cov.: 33

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.0668

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

GnomAD4 genome AF: 0.0603 AC: 9174 AN: 152200 Hom.: 406 Cov.: 33 AF XY: 0.0611 AC XY: 4547 AN XY: 74402

African (AFR) AF: 0.0140 AC: 580 AN: 41556

American (AMR) AF: 0.0497 AC: 760 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5176

South Asian (SAS) AF: 0.161 AC: 775 AN: 4822

European-Finnish (FIN) AF: 0.0930 AC: 985 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0801 AC: 5448 AN: 67978

Other (OTH) AF: 0.0665 AC: 140 AN: 2104

Alfa AF: 0.0558 Hom.: 98

Bravo AF: 0.0529

Asia WGS AF: 0.0870 AC: 303 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	1.5
DANN	Benign	0.55
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs133495; hg19: chr22-48915571;