rs11102524

Variant names:

• chr1-112725603-C-T
• rs11102524
• NM_182759.3:c.391-1026C>T

Variant summary

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

The NM_182759.3(TAFA3):​c.391-1026C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 150,328 control chromosomes in the GnomAD database, including 14,055 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 (14055 hom., cov: 26)
• Consequence: TAFA3 NM_182759.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

Genes affected

TAFA3 (HGNC:21590): (TAFA chemokine like family member 3) 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 encoding multiple isoforms 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAFA3	NM_182759.3	c.391-1026C>T		intron_variant	Intron 5 of 5	ENST00000361886.4	NP_877436.1
TAFA3	NM_001004440.2	c.459-1026C>T		intron_variant	Intron 5 of 5		NP_001004440.1
TAFA3	NR_169586.1	n.882-1026C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAFA3	ENST00000361886.4	c.391-1026C>T		intron_variant	Intron 5 of 5	1	NM_182759.3	ENSP00000355042.3
TAFA3	ENST00000369630.7	c.459-1026C>T		intron_variant	Intron 4 of 4	1		ENSP00000358644.3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 64735 AN: 150212 Hom.: 14028 Cov.: 26

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.431 AC: 64823 AN: 150328 Hom.: 14055 Cov.: 26 AF XY: 0.429 AC XY: 31480 AN XY: 73342

African (AFR) AF: 0.429 AC: 17516 AN: 40798

American (AMR) AF: 0.460 AC: 6928 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1623 AN: 3458

East Asian (EAS) AF: 0.354 AC: 1787 AN: 5054

South Asian (SAS) AF: 0.549 AC: 2597 AN: 4734

European-Finnish (FIN) AF: 0.356 AC: 3663 AN: 10290

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29342 AN: 67674

Other (OTH) AF: 0.457 AC: 943 AN: 2064

Alfa AF: 0.435 Hom.: 60771

Bravo AF: 0.436

Asia WGS AF: 0.465 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.72
DANN	Benign	0.66
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11102524; hg19: chr1-113268225;