chr22-48632756-A-G

Variant names:

• chr22-48632756-A-G
• rs5771623
• NM_001082967.3:c.113-13841A>G

Variant summary

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

The NM_001082967.3(TAFA5):​c.113-13841A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,212 control chromosomes in the GnomAD database, including 56,561 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 0.86 (56561 hom., cov: 34)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA5	NM_001082967.3	MANE Select	c.113-13841A>G		intron	N/A	NP_001076436.1
	TAFA5	NM_015381.7		c.92-13841A>G		intron	N/A	NP_056196.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA5	ENST00000402357.6	TSL:1 MANE Select	c.113-13841A>G		intron	N/A	ENSP00000383933.2
	TAFA5	ENST00000336769.9	TSL:4	c.113-13841A>G		intron	N/A	ENSP00000336812.5
	TAFA5	ENST00000358295.9	TSL:2	c.92-13841A>G		intron	N/A	ENSP00000351043.5

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130554 AN: 152094 Hom.: 56497 Cov.: 34

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.859 AC: 130679 AN: 152212 Hom.: 56561 Cov.: 34 AF XY: 0.864 AC XY: 64271 AN XY: 74410

African (AFR) AF: 0.961 AC: 39928 AN: 41548

American (AMR) AF: 0.862 AC: 13199 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2899 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4862 AN: 5144

South Asian (SAS) AF: 0.887 AC: 4280 AN: 4824

European-Finnish (FIN) AF: 0.851 AC: 9036 AN: 10620

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

European-Non Finnish (NFE) AF: 0.790 AC: 53670 AN: 67974

Other (OTH) AF: 0.847 AC: 1791 AN: 2114

Alfa AF: 0.799 Hom.: 64470

Bravo AF: 0.862

Asia WGS AF: 0.906 AC: 3148 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	1.9
DANN	Benign	0.56
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs5771623; hg19: chr22-49028568;