rs10483243

Variant names:

• chr22-48673881-C-A
• rs10483243
• NM_001082967.3:c.262+27135C>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.262+27135C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 151,928 control chromosomes in the GnomAD database, including 3,515 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 (3515 hom., cov: 32)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.25 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.262+27135C>A		intron	N/A	NP_001076436.1	Q7Z5A7-1
	TAFA5	NM_015381.7		c.241+27135C>A		intron	N/A	NP_056196.2	Q7Z5A7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA5	ENST00000402357.6	TSL:1 MANE Select	c.262+27135C>A		intron	N/A	ENSP00000383933.2	Q7Z5A7-1
	TAFA5	ENST00000336769.9	TSL:4	c.262+27135C>A		intron	N/A	ENSP00000336812.5	B1B1J6
	TAFA5	ENST00000358295.9	TSL:2	c.241+27135C>A		intron	N/A	ENSP00000351043.5	Q7Z5A7-2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32201 AN: 151810 Hom.: 3509 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.212 AC: 32235 AN: 151928 Hom.: 3515 Cov.: 32 AF XY: 0.210 AC XY: 15582 AN XY: 74242

African (AFR) AF: 0.254 AC: 10532 AN: 41392

American (AMR) AF: 0.165 AC: 2515 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.173 AC: 891 AN: 5162

South Asian (SAS) AF: 0.242 AC: 1164 AN: 4804

European-Finnish (FIN) AF: 0.197 AC: 2080 AN: 10574

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13809 AN: 67938

Other (OTH) AF: 0.203 AC: 430 AN: 2114

Alfa AF: 0.205 Hom.: 13998

Bravo AF: 0.212

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.55
PhyloP100		-0.71
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: rs10483243; hg19: chr22-49069693;