rs1352844

Variant names:

• chr4-71782032-C-T
• rs1352844
• NM_000583.4:c.58+1929G>A

Variant summary

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

The NM_000583.4(GC):​c.58+1929G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,574 control chromosomes in the GnomAD database, including 1,107 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 0.12 (1107 hom., cov: 32)
• Consequence: GC NM_000583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 18 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 (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GC	NM_000583.4	c.58+1929G>A		intron_variant	Intron 1 of 12	ENST00000273951.13	NP_000574.2
GC	NM_001204307.1	c.115+1929G>A		intron_variant	Intron 2 of 13		NP_001191236.1
GC	NM_001204306.1	c.58+1929G>A		intron_variant	Intron 2 of 13		NP_001191235.1
GC	NM_001440458.1	c.58+1929G>A		intron_variant	Intron 1 of 11		NP_001427387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000273951.13	c.58+1929G>A		intron_variant	Intron 1 of 12	1	NM_000583.4	ENSP00000273951.8

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17703 AN: 151456 Hom.: 1105 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.0647

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.117 AC: 17719 AN: 151574 Hom.: 1107 Cov.: 32 AF XY: 0.117 AC XY: 8688 AN XY: 74066

African (AFR) AF: 0.136 AC: 5641 AN: 41386

American (AMR) AF: 0.0715 AC: 1086 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0647 AC: 224 AN: 3460

East Asian (EAS) AF: 0.00156 AC: 8 AN: 5140

South Asian (SAS) AF: 0.0455 AC: 218 AN: 4796

European-Finnish (FIN) AF: 0.174 AC: 1836 AN: 10550

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8308 AN: 67750

Other (OTH) AF: 0.114 AC: 239 AN: 2102

Alfa AF: 0.118 Hom.: 3401

Bravo AF: 0.112

Asia WGS AF: 0.0310 AC: 108 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.42
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1352844; hg19: chr4-72647749;