rs222054

Variant names:

• chr4-71738582-C-G
• rs222054
• ENST00000882425.1:c.*26-2114G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-71738582-C-G
• chr4-71738582-C-T

Variant summary

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

The ENST00000882425.1(GC):​c.*26-2114G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,002 control chromosomes in the GnomAD database, including 5,749 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 0.27 (5749 hom., cov: 32)
• Consequence: GC ENST00000882425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 14 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 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.*26-2114G>C		intron	N/A	ENSP00000552484.1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40761 AN: 151884 Hom.: 5754 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.268 AC: 40774 AN: 152002 Hom.: 5749 Cov.: 32 AF XY: 0.274 AC XY: 20340 AN XY: 74290

African (AFR) AF: 0.191 AC: 7929 AN: 41462

American (AMR) AF: 0.233 AC: 3549 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1420 AN: 5148

South Asian (SAS) AF: 0.412 AC: 1980 AN: 4808

European-Finnish (FIN) AF: 0.398 AC: 4205 AN: 10568

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20025 AN: 67966

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.169 Hom.: 364

Bravo AF: 0.250

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.47
PhyloP100		-0.94

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: rs222054;

hg19: chr4-72604299;