NM_001082967.3:c.263-19642T>C

Variant names:

• chr22-48688075-T-C
• rs130110
• NM_001082967.3:c.263-19642T>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.263-19642T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 148,994 control chromosomes in the GnomAD database, including 45,860 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 0.78 (45860 hom., cov: 28)
• Consequence: TAFA5 NM_001082967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA5	NM_001082967.3	c.263-19642T>C		intron_variant	Intron 2 of 3	ENST00000402357.6	NP_001076436.1
TAFA5	NM_015381.7	c.242-19642T>C		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.263-19642T>C		intron_variant	Intron 2 of 3	1	NM_001082967.3	ENSP00000383933.2
TAFA5	ENST00000336769.9	c.263-19642T>C		intron_variant	Intron 2 of 3	4		ENSP00000336812.5
TAFA5	ENST00000358295.9	c.242-19642T>C		intron_variant	Intron 2 of 3	2		ENSP00000351043.5
TAFA5	ENST00000473898.1	n.120-19642T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.784 AC: 116698 AN: 148874 Hom.: 45821 Cov.: 28

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.784 AC: 116802 AN: 148994 Hom.: 45860 Cov.: 28 AF XY: 0.780 AC XY: 56609 AN XY: 72542

African (AFR) AF: 0.731 AC: 29916 AN: 40914

American (AMR) AF: 0.732 AC: 10559 AN: 14422

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2667 AN: 3448

East Asian (EAS) AF: 0.423 AC: 2099 AN: 4966

South Asian (SAS) AF: 0.779 AC: 3583 AN: 4598

European-Finnish (FIN) AF: 0.851 AC: 8584 AN: 10088

Middle Eastern (MID) AF: 0.748 AC: 217 AN: 290

European-Non Finnish (NFE) AF: 0.844 AC: 56815 AN: 67316

Other (OTH) AF: 0.787 AC: 1623 AN: 2062

Alfa AF: 0.819 Hom.: 72942

Bravo AF: 0.758

Asia WGS AF: 0.658 AC: 2273 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		0.28
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: rs130110; hg19: chr22-49083887;