rs4855535

Variant names:

• chr3-68885283-T-G
• rs4855535
• NM_182522.5:c.-95A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_182522.5(TAFA4):​c.-95A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,201,552 control chromosomes in the GnomAD database, including 22,778 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 0.16 (2830 hom., cov: 32)
  • Exomes 𝑓: 0.17 (19948 hom.)
• Consequence: TAFA4 NM_182522.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 13 publications found

Genes affected

TAFA4 (HGNC:21591): (TAFA chemokine like family member 4) 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. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182522.5. 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
	TAFA4	NM_182522.5	MANE Select	c.-95A>C		5_prime_UTR	Exon 2 of 6	NP_872328.1
	TAFA4	NM_001005527.3		c.-95A>C		5_prime_UTR	Exon 2 of 6	NP_001005527.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA4	ENST00000295569.12	TSL:1 MANE Select	c.-95A>C		5_prime_UTR	Exon 2 of 6	ENSP00000295569.7
	TAFA4	ENST00000495737.1	TSL:4	c.-95A>C		5_prime_UTR	Exon 2 of 4	ENSP00000419439.1
	TAFA4	ENST00000634242.1	TSL:5	c.-95A>C		5_prime_UTR	Exon 5 of 7	ENSP00000489092.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24686 AN: 151080 Hom.: 2824 Cov.: 32

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.0909

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.170 AC: 178591 AN: 1050360 Hom.: 19948 Cov.: 13 AF XY: 0.174 AC XY: 92614 AN XY: 531340

African (AFR) AF: 0.0652 AC: 1536 AN: 23574

American (AMR) AF: 0.370 AC: 9764 AN: 26414

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 1736 AN: 20228

East Asian (EAS) AF: 0.488 AC: 16863 AN: 34538

South Asian (SAS) AF: 0.312 AC: 18819 AN: 60308

European-Finnish (FIN) AF: 0.175 AC: 8261 AN: 47320

Middle Eastern (MID) AF: 0.159 AC: 746 AN: 4706

European-Non Finnish (NFE) AF: 0.143 AC: 112731 AN: 788060

Other (OTH) AF: 0.180 AC: 8135 AN: 45212

GnomAD4 genome AF: 0.163 AC: 24707 AN: 151192 Hom.: 2830 Cov.: 32 AF XY: 0.173 AC XY: 12749 AN XY: 73824

African (AFR) AF: 0.0777 AC: 3199 AN: 41150

American (AMR) AF: 0.287 AC: 4373 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0909 AC: 315 AN: 3466

East Asian (EAS) AF: 0.512 AC: 2609 AN: 5094

South Asian (SAS) AF: 0.351 AC: 1678 AN: 4780

European-Finnish (FIN) AF: 0.179 AC: 1854 AN: 10350

Middle Eastern (MID) AF: 0.152 AC: 44 AN: 290

European-Non Finnish (NFE) AF: 0.149 AC: 10107 AN: 67838

Other (OTH) AF: 0.162 AC: 341 AN: 2100

Alfa AF: 0.158 Hom.: 4025

Bravo AF: 0.165

Asia WGS AF: 0.395 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	5.9
DANN	Benign	0.67
PhyloP100		0.52
Mutation Taster		=298/2	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: rs4855535; hg19: chr3-68934434;