rs111249118

Variant names:

• chr7-100722057-CTTTT-C
• rs111249118
• NM_000799.4:c.246+21_246+24delTTTT

Your query was ambiguous. Multiple possible variants found:

• chr7-100722057-CTTTT-C
• chr7-100722057-CTTTT-CT
• chr7-100722057-CTTTT-CTT
• chr7-100722057-CTTTT-CTTT
• chr7-100722057-CTTTT-CTTTTT
• chr7-100722057-CTTTT-CTTTTTT
• chr7-100722057-CTTTT-CTTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000799.4(EPO):​c.246+21_246+24delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000034 in 1,381,958 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 0.000028 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000035 (0 hom.)
• Consequence: EPO NM_000799.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

Genes affected

EPO (HGNC:3415): (erythropoietin) This gene encodes a secreted, glycosylated cytokine composed of four alpha helical bundles. The encoded protein is mainly synthesized in the kidney, secreted into the blood plasma, and binds to the erythropoietin receptor to promote red blood cell production, or erythropoiesis, in the bone marrow. Expression of this gene is upregulated under hypoxic conditions, in turn leading to increased erythropoiesis and enhanced oxygen-carrying capacity of the blood. Expression of this gene has also been observed in brain and in the eye, and elevated expression levels have been observed in diabetic retinopathy and ocular hypertension. Recombinant forms of the encoded protein exhibit neuroprotective activity against a variety of potential brain injuries, as well as antiapoptotic functions in several tissue types, and have been used in the treatment of anemia and to enhance the efficacy of cancer therapies. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPO	NM_000799.4	c.246+21_246+24delTTTT		intron_variant	Intron 3 of 4	ENST00000252723.3	NP_000790.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPO	ENST00000252723.3	c.246+10_246+13delTTTT		intron_variant	Intron 3 of 4	1	NM_000799.4	ENSP00000252723.2

Frequencies

GnomAD3 genomes AF: 0.0000284 AC: 4 AN: 140912 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000103

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000346 AC: 43 AN: 1241046 Hom.: 0 AF XY: 0.0000322 AC XY: 20 AN XY: 620492

Gnomad4 AFR exome AF: 0.0000727

Gnomad4 AMR exome AF: 0.0000702

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000545

Gnomad4 SAS exome AF: 0.0000139

Gnomad4 FIN exome AF: 0.000249

Gnomad4 NFE exome AF: 0.0000241

Gnomad4 OTH exome AF: 0.0000384

GnomAD4 genome AF: 0.0000284 AC: 4 AN: 140912 Hom.: 0 Cov.: 31 AF XY: 0.0000439 AC XY: 3 AN XY: 68278

Gnomad4 AFR AF: 0.000103

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs111249118; hg19: chr7-100319680;