22-48503032-G-A

Variant names:

• chr22-48503032-G-A
• rs6008743
• NM_001082967.3:c.112+13328G>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+13328G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,154 control chromosomes in the GnomAD database, including 7,789 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 0.26 (7789 hom., cov: 33)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001082967.3. 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
	TAFA5	NM_001082967.3	MANE Select	c.112+13328G>A		intron	N/A	NP_001076436.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA5	ENST00000402357.6	TSL:1 MANE Select	c.112+13328G>A		intron	N/A	ENSP00000383933.2
	TAFA5	ENST00000336769.9	TSL:4	c.112+13328G>A		intron	N/A	ENSP00000336812.5
	TAFA5	ENST00000912217.1		c.112+13328G>A		intron	N/A	ENSP00000582276.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38750 AN: 152036 Hom.: 7762 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.255 AC: 38826 AN: 152154 Hom.: 7789 Cov.: 33 AF XY: 0.247 AC XY: 18395 AN XY: 74386

African (AFR) AF: 0.564 AC: 23389 AN: 41482

American (AMR) AF: 0.143 AC: 2188 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.0757 AC: 391 AN: 5162

South Asian (SAS) AF: 0.107 AC: 517 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1349 AN: 10610

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10149 AN: 68004

Other (OTH) AF: 0.209 AC: 440 AN: 2110

Alfa AF: 0.237 Hom.: 812

Bravo AF: 0.266

Asia WGS AF: 0.118 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.42
PhyloP100		-0.16
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: rs6008743; hg19: chr22-48898844;