rs16847047

Variant names:

• chr4-71789458-C-T
• rs16847047
• ENST00000504199.5:c.22-5404G>A

Variant summary

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

The ENST00000504199.5(GC):​c.22-5404G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,818 control chromosomes in the GnomAD database, including 1,036 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 0.11 (1036 hom., cov: 32)
• Consequence: GC ENST00000504199.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504199.5. 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
	GC	NM_001204307.1		c.22-5404G>A		intron	N/A	NP_001191236.1
	GC	NM_001204306.1		c.-36-5404G>A		intron	N/A	NP_001191235.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GC	ENST00000504199.5	TSL:1	c.22-5404G>A		intron	N/A	ENSP00000421725.1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17215 AN: 151700 Hom.: 1034 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0641

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.113 AC: 17229 AN: 151818 Hom.: 1036 Cov.: 32 AF XY: 0.114 AC XY: 8475 AN XY: 74184

African (AFR) AF: 0.132 AC: 5453 AN: 41442

American (AMR) AF: 0.0690 AC: 1050 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0641 AC: 222 AN: 3464

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5152

South Asian (SAS) AF: 0.0424 AC: 204 AN: 4814

European-Finnish (FIN) AF: 0.172 AC: 1820 AN: 10554

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.119 AC: 8085 AN: 67874

Other (OTH) AF: 0.109 AC: 230 AN: 2104

Alfa AF: 0.119 Hom.: 149

Bravo AF: 0.108

Asia WGS AF: 0.0310 AC: 109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.63
DANN	Benign	0.28
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16847047; hg19: chr4-72655175;