ENST00000882425.1:c.*880A>G

Variant names:

• chr4-71735614-T-C
• rs12512631
• ENST00000882425.1:c.*880A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000882425.1(GC):​c.*880A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,028 control chromosomes in the GnomAD database, including 9,424 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 0.35 (9424 hom., cov: 32)
• Consequence: GC ENST00000882425.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 58 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000882425.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GC	ENST00000882425.1		c.*880A>G		3_prime_UTR	Exon 13 of 13	ENSP00000552484.1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53267 AN: 151912 Hom.: 9424 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.351 AC: 53296 AN: 152028 Hom.: 9424 Cov.: 32 AF XY: 0.352 AC XY: 26128 AN XY: 74332

African (AFR) AF: 0.345 AC: 14289 AN: 41458

American (AMR) AF: 0.417 AC: 6379 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1472 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1083 AN: 5160

South Asian (SAS) AF: 0.259 AC: 1249 AN: 4826

European-Finnish (FIN) AF: 0.373 AC: 3944 AN: 10560

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23681 AN: 67956

Other (OTH) AF: 0.365 AC: 770 AN: 2110

Alfa AF: 0.353 Hom.: 30009

Bravo AF: 0.355

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.79
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs12512631; hg19: chr4-72601331;