rs7410750

Variant names:

• chr22-48832695-G-T
• rs7410750
• ENST00000336769.9:c.391-18063G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000336769.9(TAFA5):​c.391-18063G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,028 control chromosomes in the GnomAD database, including 13,998 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 0.43 (13998 hom., cov: 33)
• Consequence: TAFA5 ENST00000336769.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000336769.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAFA5	ENST00000336769.9	TSL:4	c.391-18063G>T		intron	N/A	ENSP00000336812.5

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64550 AN: 151910 Hom.: 13980 Cov.: 33

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.425 AC: 64616 AN: 152028 Hom.: 13998 Cov.: 33 AF XY: 0.425 AC XY: 31565 AN XY: 74290

African (AFR) AF: 0.483 AC: 20013 AN: 41454

American (AMR) AF: 0.366 AC: 5596 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1233 AN: 5178

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4814

European-Finnish (FIN) AF: 0.466 AC: 4918 AN: 10548

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28523 AN: 67954

Other (OTH) AF: 0.416 AC: 877 AN: 2108

Alfa AF: 0.415 Hom.: 6892

Bravo AF: 0.418

Asia WGS AF: 0.339 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.63
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7410750; hg19: chr22-49228507;