rs5771716

Variant names:

• chr22-48684963-G-A
• rs5771716
• NM_001082967.3:c.263-22754G>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.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
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 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.263-22754G>A		intron	N/A	NP_001076436.1	Q7Z5A7-1
	TAFA5	NM_015381.7		c.242-22754G>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.263-22754G>A		intron	N/A	ENSP00000383933.2	Q7Z5A7-1
	TAFA5	ENST00000336769.9	TSL:4	c.263-22754G>A		intron	N/A	ENSP00000336812.5	B1B1J6
	TAFA5	ENST00000358295.9	TSL:2	c.242-22754G>A		intron	N/A	ENSP00000351043.5	Q7Z5A7-2

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

African (AFR) AF: 0.344 AC: 14284 AN: 41486

American (AMR) AF: 0.650 AC: 9923 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1800 AN: 5170

South Asian (SAS) AF: 0.649 AC: 3127 AN: 4820

European-Finnish (FIN) AF: 0.658 AC: 6943 AN: 10546

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46452 AN: 67986

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.647 Hom.: 125664

Bravo AF: 0.559

Asia WGS AF: 0.493 AC: 1713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.35
PhyloP100		-0.81
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: rs5771716; hg19: chr22-49080775;