rs16847054

Variant names:

• chr4-71803242-C-T
• rs16847054
• ENST00000504199.5:c.21+684G>A

Variant summary

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

The ENST00000504199.5(GC):​c.21+684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 152,130 control chromosomes in the GnomAD database, including 564 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 0.081 (564 hom., cov: 33)
• Consequence: GC ENST00000504199.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GC	NM_001204307.1	c.21+684G>A		intron_variant	Intron 1 of 13		NP_001191236.1
GC	NM_001204306.1	c.-37+2100G>A		intron_variant	Intron 1 of 13		NP_001191235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000504199.5	c.21+684G>A		intron_variant	Intron 1 of 13	1		ENSP00000421725.1

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12261 AN: 152010 Hom.: 562 Cov.: 33

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.0330

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0892

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

GnomAD4 genome AF: 0.0806 AC: 12268 AN: 152130 Hom.: 564 Cov.: 33 AF XY: 0.0791 AC XY: 5885 AN XY: 74374

African (AFR) AF: 0.0977 AC: 4056 AN: 41502

American (AMR) AF: 0.0868 AC: 1327 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1166 AN: 5170

South Asian (SAS) AF: 0.0917 AC: 442 AN: 4820

European-Finnish (FIN) AF: 0.0330 AC: 350 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0631 AC: 4286 AN: 67974

Other (OTH) AF: 0.0891 AC: 188 AN: 2110

Alfa AF: 0.0709 Hom.: 65

Bravo AF: 0.0886

Asia WGS AF: 0.126 AC: 436 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.21
PhyloP100		-0.37
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: rs16847054; hg19: chr4-72668959;