NM_182522.5:c.-122-11227T>C

Variant names:

• chr3-68896537-A-G
• rs9847748
• NM_182522.5:c.-122-11227T>C

Variant summary

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

The NM_182522.5(TAFA4):​c.-122-11227T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,118 control chromosomes in the GnomAD database, including 17,375 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 0.46 (17375 hom., cov: 33)
• Consequence: TAFA4 NM_182522.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA4	NM_182522.5	c.-122-11227T>C		intron_variant	Intron 1 of 5	ENST00000295569.12	NP_872328.1
TAFA4	NM_001005527.3	c.-122-11227T>C		intron_variant	Intron 1 of 5		NP_001005527.1
TAFA4	XM_011533371.2	c.-122-11227T>C		intron_variant	Intron 1 of 5		XP_011531673.1
TAFA4	XM_011533372.2	c.-122-11227T>C		intron_variant	Intron 1 of 5		XP_011531674.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA4	ENST00000295569.12	c.-122-11227T>C		intron_variant	Intron 1 of 5	1	NM_182522.5	ENSP00000295569.7
TAFA4	ENST00000495737.1	c.-122-11227T>C		intron_variant	Intron 1 of 3	4		ENSP00000419439.1
TAFA4	ENST00000634242.1	c.-122-11227T>C		intron_variant	Intron 4 of 6	5		ENSP00000489092.1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69493 AN: 152000 Hom.: 17341 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.457 AC: 69585 AN: 152118 Hom.: 17375 Cov.: 33 AF XY: 0.462 AC XY: 34324 AN XY: 74366

African (AFR) AF: 0.596 AC: 24710 AN: 41464

American (AMR) AF: 0.546 AC: 8352 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.815 AC: 4220 AN: 5180

South Asian (SAS) AF: 0.490 AC: 2365 AN: 4824

European-Finnish (FIN) AF: 0.340 AC: 3605 AN: 10594

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24100 AN: 67980

Other (OTH) AF: 0.419 AC: 884 AN: 2110

Alfa AF: 0.409 Hom.: 22767

Bravo AF: 0.477

Asia WGS AF: 0.651 AC: 2257 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.49
PhyloP100		0.028
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: rs9847748; hg19: chr3-68945688;