Genetic Variant GC:p.Thr436Arg (chr4-71752605-CGT-TCG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_000583.4(GC):c.1306_1308delACGinsCGA(p.Thr436Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T436K) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

GC
NM_000583.4 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.459

Publications

0 publications found

Variant links:

Genes affected

GC (HGNC:4187): (GC vitamin D binding protein) The protein encoded by this gene belongs to the albumin gene family. It is a multifunctional protein found in plasma, ascitic fluid, cerebrospinal fluid and on the surface of many cell types. It binds to vitamin D and its plasma metabolites and transports them to target tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]

GC links:

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new If you want to explore the variant's impact on the transcript NM_000583.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000583.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GC	NM_000583.4	MANE Select	c.1306_1308delACGinsCGA	p.Thr436Arg	missense	N/A	NP_000574.2
GC	NM_001204307.1		c.1363_1365delACGinsCGA	p.Thr455Arg	missense	N/A	NP_001191236.1	P02774-3
GC	NM_001204306.1		c.1306_1308delACGinsCGA	p.Thr436Arg	missense	N/A	NP_001191235.1	P02774-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GC	ENST00000273951.13	TSL:1 MANE Select	c.1306_1308delACGinsCGA	p.Thr436Arg	missense	N/A	ENSP00000273951.8	P02774-1
GC	ENST00000504199.5	TSL:1	c.1363_1365delACGinsCGA	p.Thr455Arg	missense	N/A	ENSP00000421725.1	P02774-3
GC	ENST00000513476.5	TSL:5	c.1306_1308delACGinsCGA	p.Thr436Arg	missense	N/A	ENSP00000426683.1	D6RF35

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over