4-71783331-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000583.4(GC):c.58+630T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,666 control chromosomes in the GnomAD database, including 4,301 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 (4301 hom., cov: 32)
• Consequence: GC NM_000583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GC	NM_000583.4	c.58+630T>C		intron_variant		ENST00000273951.13
GC	NM_001204306.1	c.58+630T>C		intron_variant
GC	NM_001204307.1	c.115+630T>C		intron_variant
GC	XM_006714177.3	c.58+630T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GC	ENST00000273951.13	c.58+630T>C		intron_variant		1	NM_000583.4	P1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33910 AN: 151548 Hom.: 4302 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.224 AC: 33913 AN: 151666 Hom.: 4301 Cov.: 32 AF XY: 0.221 AC XY: 16359 AN XY: 74152

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.233

Alfa AF: 0.256 Hom.: 1048

Bravo AF: 0.222

Asia WGS AF: 0.268 AC: 934 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.040
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs221999; hg19: chr4-72649048;