NM_032862.5:c.29C>A

Variant names:

• chr8-143597932-C-A
• rs964458641
• NM_032862.5:c.29C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032862.5(TIGD5):​c.29C>A​(p.Pro10Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 867,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000048 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000049 (0 hom.)
• Consequence: TIGD5 NM_032862.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.299
• Publications: 1 publications found

Genes affected

TIGD5 (HGNC:18336): (tigger transposable element derived 5) The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. The exact function of this gene is not known. [provided by RefSeq, Jul 2008]

EEF1D (HGNC:3211): (eukaryotic translation elongation factor 1 delta) This gene encodes a subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This subunit, delta, functions as guanine nucleotide exchange factor. It is reported that following HIV-1 infection, this subunit interacts with HIV-1 Tat. This interaction results in repression of translation of host cell proteins and enhanced translation of viral proteins. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. Related pseudogenes have been defined on chromosomes 1, 6, 7, 9, 11, 13, 17, 19.[provided by RefSeq, Aug 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2061202).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032862.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIGD5	NM_032862.5	MANE Select	c.29C>A	p.Pro10Gln	missense	Exon 1 of 1	NP_116251.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIGD5	ENST00000504548.4	TSL:6 MANE Select	c.29C>A	p.Pro10Gln	missense	Exon 1 of 1	ENSP00000421489.2	Q53EQ6-1
	EEF1D	ENST00000972259.1		c.-180+1001G>T		intron	N/A	ENSP00000642318.1
	EEF1D	ENST00000972260.1		c.-1+1001G>T		intron	N/A	ENSP00000642319.1

Frequencies

GnomAD3 genomes AF: 0.0000481 AC: 7 AN: 145592 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000763

Gnomad OTH AF: 0.000997

GnomAD4 exome AF: 0.0000485 AC: 35 AN: 721624 Hom.: 0 Cov.: 9 AF XY: 0.0000478 AC XY: 16 AN XY: 334884

African (AFR) AF: 0.00 AC: 0 AN: 13794

American (AMR) AF: 0.00 AC: 0 AN: 834

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4440

East Asian (EAS) AF: 0.00 AC: 0 AN: 3148

South Asian (SAS) AF: 0.00 AC: 0 AN: 15040

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 242

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1420

European-Non Finnish (NFE) AF: 0.0000516 AC: 34 AN: 659132

Other (OTH) AF: 0.0000424 AC: 1 AN: 23574

GnomAD4 genome AF: 0.0000481 AC: 7 AN: 145592 Hom.: 0 Cov.: 32 AF XY: 0.0000283 AC XY: 2 AN XY: 70794

African (AFR) AF: 0.00 AC: 0 AN: 40688

American (AMR) AF: 0.00 AC: 0 AN: 14704

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3374

East Asian (EAS) AF: 0.00 AC: 0 AN: 5066

South Asian (SAS) AF: 0.00 AC: 0 AN: 4786

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8226

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.0000763 AC: 5 AN: 65526

Other (OTH) AF: 0.000997 AC: 2 AN: 2006

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.000113

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	17
DANN	Benign	0.91
DEOGEN2	Benign	0.012	T
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.51
FATHMM_MKL	Benign	0.011	N
LIST_S2	Benign	0.25	T
M_CAP	Pathogenic	0.46	D
MetaRNN	Benign	0.21	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.81	L
PhyloP100		-0.30
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-0.55	N
REVEL	Benign	0.11
Sift	Uncertain	0.011	D
Sift4G	Uncertain	0.015	D
Vest4		0.24
MutPred		0.19		Gain of MoRF binding (P = 0.0153)
MVP		0.38
MPC		0.76
ClinPred		0.16	T
GERP RS		4.4
PromoterAI		0.054	Neutral
Varity_R		0.071
gMVP		0.28
Mutation Taster		=298/2	polymorphism

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: rs964458641; hg19: chr8-144680102;