ENST00000414723.1:c.364-3295A>T

Variant names:

• chr2-162356256-T-.
• NM_012198.5:c.263-182T>.

Variant summary

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

The ENST00000414723.1(GCA):​c.-184T>. variant causes a upstream gene change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: GCA ENST00000414723.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: No publications found

Genes affected

GCA (HGNC:15990): (grancalcin) This gene encodes a calcium-binding protein that is abundant in neutrophils and macrophages. In the absence of divalent cation, this protein localizes to the cytosolic fraction; with magnesium alone, it partitions with the granule fraction; and in the presence of magnesium and calcium, it associates with both the granule and membrane fractions. Alternative splicing and use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Aug 2016]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414723.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCA	NM_012198.5	MANE Select	c.263-182T>.		intron	N/A	NP_036330.1
	GCA	NM_001330268.1		c.341-182T>.		intron	N/A	NP_001317197.1
	GCA	NM_001330265.1		c.308-182T>.		intron	N/A	NP_001317194.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GCA	ENST00000437150.7	TSL:1 MANE Select	c.263-182T>.		intron	N/A	ENSP00000394842.2
	GCA	ENST00000233612.8	TSL:2	c.206-182T>.		intron	N/A	ENSP00000233612.4
	GCA	ENST00000446271.5	TSL:5	c.341-182T>.		intron	N/A	ENSP00000393218.1

Frequencies

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Splicing

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

Other links and lift over

hg19: chr2-163212766;