3-27721936-G-GCGGCGGCGGCGC

Variant names:

• chr3-27721936-G-GCGGCGGCGGCGC
• rs1553745484
• NM_001278182.2:c.358_359insGCGCCGCCGCCG

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3 BS2

The NM_001278182.2(EOMES):​c.358_359insGCGCCGCCGCCG​(p.Ala119_Ala120insGlyAlaAlaAla) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000227 in 1,364,254 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000053 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000019 (0 hom.)
• Consequence: EOMES NM_001278182.2 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

EOMES (HGNC:3372): (eomesodermin) This gene belongs to the TBR1 (T-box brain protein 1) sub-family of T-box genes that share the common DNA-binding T-box domain. The encoded protein is a transcription factor which is crucial for embryonic development of mesoderm and the central nervous system in vertebrates. The protein may also be necessary for the differentiation of effector CD8+ T cells which are involved in defense against viral infections. A similar gene disrupted in mice is shown to be essential during trophoblast development and gastrulation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001278182.2
• BS2: High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EOMES	NM_001278182.2	c.358_359insGCGCCGCCGCCG	p.Ala119_Ala120insGlyAlaAlaAla	conservative_inframe_insertion	Exon 1 of 6	ENST00000449599.4	NP_001265111.1
EOMES	NM_005442.4	c.358_359insGCGCCGCCGCCG	p.Ala119_Ala120insGlyAlaAlaAla	conservative_inframe_insertion	Exon 1 of 6		NP_005433.2
EOMES	XM_005265510.5	c.358_359insGCGCCGCCGCCG	p.Ala119_Ala120insGlyAlaAlaAla	conservative_inframe_insertion	Exon 1 of 7		XP_005265567.1
EOMES	NM_001278183.2	c.-5+493_-5+494insGCGCCGCCGCCG		intron_variant	Intron 1 of 5		NP_001265112.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EOMES	ENST00000449599.4	c.358_359insGCGCCGCCGCCG	p.Ala119_Ala120insGlyAlaAlaAla	conservative_inframe_insertion	Exon 1 of 6	1	NM_001278182.2	ENSP00000388620.1
EOMES	ENST00000295743.8	c.358_359insGCGCCGCCGCCG	p.Ala119_Ala120insGlyAlaAlaAla	conservative_inframe_insertion	Exon 1 of 6	1		ENSP00000295743.4
EOMES	ENST00000461503.2	c.-5+493_-5+494insGCGCCGCCGCCG		intron_variant	Intron 1 of 5	2		ENSP00000487112.1

Frequencies

GnomAD3 genomes AF: 0.0000530 AC: 8 AN: 151026 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000660

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000401

Gnomad SAS AF: 0.000416

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000443

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000190 AC: 23 AN: 1213118 Hom.: 0 Cov.: 35 AF XY: 0.0000254 AC XY: 15 AN XY: 591020

Gnomad4 AFR exome AF: 0.0000842

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000382

Gnomad4 SAS exome AF: 0.0000230

Gnomad4 FIN exome AF: 0.0000239

Gnomad4 NFE exome AF: 0.0000170

Gnomad4 OTH exome AF: 0.0000202

GnomAD4 genome AF: 0.0000529 AC: 8 AN: 151136 Hom.: 0 Cov.: 0 AF XY: 0.0000677 AC XY: 5 AN XY: 73802

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000659

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000402

Gnomad4 SAS AF: 0.000417

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000443

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1553745484; hg19: chr3-27763427;