chr22-48720986-G-C

Variant names:

• chr22-48720986-G-C
• rs960362
• NM_001082967.3:c.390+13142G>C

Variant summary

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

The NM_001082967.3(TAFA5):​c.390+13142G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,118 control chromosomes in the GnomAD database, including 4,040 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 0.22 (4040 hom., cov: 33)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA5	NM_001082967.3	c.390+13142G>C		intron_variant	Intron 3 of 3	ENST00000402357.6	NP_001076436.1
TAFA5	NM_015381.7	c.369+13142G>C		intron_variant	Intron 3 of 3		NP_056196.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA5	ENST00000402357.6	c.390+13142G>C		intron_variant	Intron 3 of 3	1	NM_001082967.3	ENSP00000383933.2

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33950 AN: 152000 Hom.: 4040 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.223 AC: 33972 AN: 152118 Hom.: 4040 Cov.: 33 AF XY: 0.221 AC XY: 16420 AN XY: 74382

African (AFR) AF: 0.226 AC: 9391 AN: 41506

American (AMR) AF: 0.318 AC: 4869 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3468

East Asian (EAS) AF: 0.106 AC: 544 AN: 5156

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4818

European-Finnish (FIN) AF: 0.156 AC: 1650 AN: 10596

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14505 AN: 67964

Other (OTH) AF: 0.205 AC: 434 AN: 2112

Alfa AF: 0.0775 Hom.: 119

Bravo AF: 0.235

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.099
DANN	Benign	0.57
PhyloP100		-1.9
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: rs960362; hg19: chr22-49116798;