rs5771716

Positions:

• chr22-48684963-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001082967.3(TAFA5):​c.263-22754G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,064 control chromosomes in the GnomAD database, including 26,557 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 0.57 (26557 hom., cov: 32)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAFA5	NM_001082967.3	c.263-22754G>A		intron_variant		ENST00000402357.6
TAFA5	NM_015381.7	c.242-22754G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAFA5	ENST00000402357.6	c.263-22754G>A		intron_variant		1	NM_001082967.3	P4
TAFA5	ENST00000336769.9	c.263-22754G>A		intron_variant		4
TAFA5	ENST00000358295.9	c.242-22754G>A		intron_variant		2		A1
TAFA5	ENST00000473898.1	n.120-22754G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86709 AN: 151944 Hom.: 26563 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.570 AC: 86737 AN: 152064 Hom.: 26557 Cov.: 32 AF XY: 0.570 AC XY: 42329 AN XY: 74306

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.596

Alfa AF: 0.663 Hom.: 53952

Bravo AF: 0.559

Asia WGS AF: 0.493 AC: 1713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.35

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

Publications

LitVar

Other links and lift over

dbSNP: rs5771716; hg19: chr22-49080775;