rs17467825

Variant names:

• chr4-71739800-A-G
• rs17467825
• ENST00000882425.1:c.*26-3332T>C

Variant summary

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

The ENST00000882425.1(GC):​c.*26-3332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,142 control chromosomes in the GnomAD database, including 4,287 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 0.22 (4287 hom., cov: 32)
• Consequence: GC ENST00000882425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 67 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 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.*26-3332T>C		intron	N/A	ENSP00000552484.1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33313 AN: 152024 Hom.: 4283 Cov.: 32

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.219 AC: 33334 AN: 152142 Hom.: 4287 Cov.: 32 AF XY: 0.214 AC XY: 15951 AN XY: 74372

African (AFR) AF: 0.0917 AC: 3806 AN: 41520

American (AMR) AF: 0.223 AC: 3407 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1311 AN: 5160

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4814

European-Finnish (FIN) AF: 0.186 AC: 1964 AN: 10582

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19560 AN: 67994

Other (OTH) AF: 0.230 AC: 486 AN: 2114

Alfa AF: 0.264 Hom.: 8949

Bravo AF: 0.215

Asia WGS AF: 0.225 AC: 786 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.66
PhyloP100		0.21

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.

Other links and lift over

dbSNP: rs17467825;

hg19: chr4-72605517;