rs6752614

Positions:

• chr2-232549061-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.822G>A​(p.Ala274=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 712,134 control chromosomes in the GnomAD database, including 88,489 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 0.44 (15564 hom., cov: 33)
  • Exomes 𝑓: 0.50 (72925 hom.)
• Consequence: TIGD1 NM_145702.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.58).
• BP7: Synonymous conserved (PhyloP=-1.28 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TIGD1	NM_145702.4	c.822G>A	p.Ala274=	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.822G>A	p.Ala274=	synonymous_variant	1/1		NM_145702.4	ENSP00000386186	P1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66521 AN: 151982 Hom.: 15552 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.478

GnomAD3 exomes AF: 0.523 AC: 77634 AN: 148544 Hom.: 21123 AF XY: 0.525 AC XY: 41259 AN XY: 78556

Gnomad AFR exome AF: 0.260

Gnomad AMR exome AF: 0.663

Gnomad ASJ exome AF: 0.557

Gnomad EAS exome AF: 0.576

Gnomad SAS exome AF: 0.575

Gnomad FIN exome AF: 0.469

Gnomad NFE exome AF: 0.478

Gnomad OTH exome AF: 0.526

GnomAD4 exome AF: 0.504 AC: 282133 AN: 560034 Hom.: 72925 Cov.: 0 AF XY: 0.509 AC XY: 153605 AN XY: 301972

Gnomad4 AFR exome AF: 0.268

Gnomad4 AMR exome AF: 0.653

Gnomad4 ASJ exome AF: 0.555

Gnomad4 EAS exome AF: 0.581

Gnomad4 SAS exome AF: 0.579

Gnomad4 FIN exome AF: 0.468

Gnomad4 NFE exome AF: 0.480

Gnomad4 OTH exome AF: 0.494

GnomAD4 genome AF: 0.438 AC: 66552 AN: 152100 Hom.: 15564 Cov.: 33 AF XY: 0.442 AC XY: 32889 AN XY: 74362

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.483

Alfa AF: 0.477 Hom.: 5691

Bravo AF: 0.441

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	3.3
DANN	Benign	0.91

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: rs6752614; hg19: chr2-233413771; COSMIC: COSV51471993; COSMIC: COSV51471993;