rs1489992

Variant names:

• chr3-68755873-T-A
• rs1489992
• NM_182522.5:c.131-2855A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-68755873-T-A
• chr3-68755873-T-C
• chr3-68755873-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_182522.5(TAFA4):​c.131-2855A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TAFA4 NM_182522.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA4	NM_182522.5	c.131-2855A>T		intron_variant	Intron 3 of 5	ENST00000295569.12	NP_872328.1
TAFA4	NM_001005527.3	c.131-2855A>T		intron_variant	Intron 3 of 5		NP_001005527.1
TAFA4	XM_011533371.2	c.131-2855A>T		intron_variant	Intron 3 of 5		XP_011531673.1
TAFA4	XM_011533372.2	c.131-2855A>T		intron_variant	Intron 3 of 5		XP_011531674.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA4	ENST00000295569.12	c.131-2855A>T		intron_variant	Intron 3 of 5	1	NM_182522.5	ENSP00000295569.7
TAFA4	ENST00000495737.1	c.131-2855A>T		intron_variant	Intron 3 of 3	4		ENSP00000419439.1
TAFA4	ENST00000634242.1	c.131-2855A>T		intron_variant	Intron 6 of 6	5		ENSP00000489092.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.073
DANN	Benign	0.55

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: rs1489992; hg19: chr3-68805024;