22-48672561-G-T

Variant names:

• chr22-48672561-G-T
• rs5771932
• NM_001082967.3:c.262+25815G>T

Variant summary

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

The NM_001082967.3(TAFA5):​c.262+25815G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,082 control chromosomes in the GnomAD database, including 3,413 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 0.21 (3413 hom., cov: 33)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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.262+25815G>T		intron	N/A	NP_001076436.1
	TAFA5	NM_015381.7		c.241+25815G>T		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.262+25815G>T		intron	N/A	ENSP00000383933.2
	TAFA5	ENST00000336769.9	TSL:4	c.262+25815G>T		intron	N/A	ENSP00000336812.5
	TAFA5	ENST00000358295.9	TSL:2	c.241+25815G>T		intron	N/A	ENSP00000351043.5

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31806 AN: 151964 Hom.: 3409 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.209 AC: 31833 AN: 152082 Hom.: 3413 Cov.: 33 AF XY: 0.207 AC XY: 15424 AN XY: 74374

African (AFR) AF: 0.247 AC: 10246 AN: 41458

American (AMR) AF: 0.163 AC: 2498 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3466

East Asian (EAS) AF: 0.173 AC: 895 AN: 5180

South Asian (SAS) AF: 0.243 AC: 1172 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2099 AN: 10578

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13682 AN: 67968

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.118 Hom.: 174

Bravo AF: 0.208

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.63
PhyloP100		1.0
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: rs5771932; hg19: chr22-49068373;