rs5771675

Variant names:

• chr22-48650463-A-G
• rs5771675
• NM_001082967.3:c.262+3717A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-48650463-A-G
• chr22-48650463-A-T

Variant summary

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

The NM_001082967.3(TAFA5):​c.262+3717A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,904 control chromosomes in the GnomAD database, including 21,423 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 0.53 (21423 hom., cov: 32)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA5	NM_001082967.3	c.262+3717A>G		intron_variant	Intron 2 of 3	ENST00000402357.6	NP_001076436.1
TAFA5	NM_015381.7	c.241+3717A>G		intron_variant	Intron 2 of 3		NP_056196.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA5	ENST00000402357.6	c.262+3717A>G		intron_variant	Intron 2 of 3	1	NM_001082967.3	ENSP00000383933.2
TAFA5	ENST00000336769.9	c.262+3717A>G		intron_variant	Intron 2 of 3	4		ENSP00000336812.5
TAFA5	ENST00000358295.9	c.241+3717A>G		intron_variant	Intron 2 of 3	2		ENSP00000351043.5
TAFA5	ENST00000473898.1	n.120-57254A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79805 AN: 151784 Hom.: 21419 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.526 AC: 79855 AN: 151904 Hom.: 21423 Cov.: 32 AF XY: 0.529 AC XY: 39241 AN XY: 74204

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.529

Alfa AF: 0.435 Hom.: 2190

Bravo AF: 0.533

Asia WGS AF: 0.544 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.098
DANN	Benign	0.21

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: rs5771675; hg19: chr22-49046275;