2-232549631-C-T

Position:

• chr2-232549631-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_145702.4(TIGD1):​c.252G>A​(p.Lys84Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 706,670 control chromosomes in the GnomAD database, including 76,909 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 0.40 (13214 hom., cov: 33)
  • Exomes 𝑓: 0.47 (63695 hom.)
• Consequence: TIGD1 NM_145702.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

Genes affected

TIGD1 (HGNC:14523): (tigger transposable element derived 1) 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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP7: Synonymous conserved (PhyloP=-0.372 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TIGD1	NM_145702.4	c.252G>A	p.Lys84Lys	synonymous_variant	1/1	ENST00000408957.7	NP_663748.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TIGD1	ENST00000408957.7	c.252G>A	p.Lys84Lys	synonymous_variant	1/1	6	NM_145702.4	ENSP00000386186.3

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60214 AN: 151954 Hom.: 13199 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.431

GnomAD3 exomes AF: 0.490 AC: 67051 AN: 136798 Hom.: 17207 AF XY: 0.494 AC XY: 36291 AN XY: 73444

Gnomad AFR exome AF: 0.187

Gnomad AMR exome AF: 0.596

Gnomad ASJ exome AF: 0.550

Gnomad EAS exome AF: 0.501

Gnomad SAS exome AF: 0.544

Gnomad FIN exome AF: 0.442

Gnomad NFE exome AF: 0.458

Gnomad OTH exome AF: 0.494

GnomAD4 exome AF: 0.473 AC: 262380 AN: 554598 Hom.: 63695 Cov.: 4 AF XY: 0.479 AC XY: 143519 AN XY: 299628

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.587

Gnomad4 ASJ exome AF: 0.547

Gnomad4 EAS exome AF: 0.472

Gnomad4 SAS exome AF: 0.549

Gnomad4 FIN exome AF: 0.437

Gnomad4 NFE exome AF: 0.461

Gnomad4 OTH exome AF: 0.461

GnomAD4 genome AF: 0.396 AC: 60234 AN: 152072 Hom.: 13214 Cov.: 33 AF XY: 0.401 AC XY: 29783 AN XY: 74320

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.436

Alfa AF: 0.383 Hom.: 1954

Bravo AF: 0.395

Asia WGS AF: 0.540 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	8.6
DANN	Benign	0.93

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

Publications

LitVar

Other links and lift over

dbSNP: rs4973540; hg19: chr2-233414341;