rs222020

Variant names:

• chr4-71770555-C-T
• rs222020
• NM_000583.4:c.59-1155G>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.59-1155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 151,872 control chromosomes in the GnomAD database, including 42,344 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 0.73 (42344 hom., cov: 31)
• Consequence: GC NM_000583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 49 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GC	NM_000583.4	c.59-1155G>A		intron_variant	Intron 1 of 12	ENST00000273951.13	NP_000574.2
GC	NM_001204307.1	c.116-1155G>A		intron_variant	Intron 2 of 13		NP_001191236.1
GC	NM_001204306.1	c.59-1155G>A		intron_variant	Intron 2 of 13		NP_001191235.1
GC	NM_001440458.1	c.59-1155G>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.59-1155G>A		intron_variant	Intron 1 of 12	1	NM_000583.4	ENSP00000273951.8

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110277 AN: 151754 Hom.: 42341 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.726 AC: 110312 AN: 151872 Hom.: 42344 Cov.: 31 AF XY: 0.727 AC XY: 53990 AN XY: 74244

African (AFR) AF: 0.457 AC: 18890 AN: 41330

American (AMR) AF: 0.808 AC: 12330 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3139 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3083 AN: 5130

South Asian (SAS) AF: 0.854 AC: 4115 AN: 4816

European-Finnish (FIN) AF: 0.796 AC: 8420 AN: 10580

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57762 AN: 67972

Other (OTH) AF: 0.760 AC: 1597 AN: 2102

Alfa AF: 0.799 Hom.: 119301

Bravo AF: 0.708

Asia WGS AF: 0.701 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		-0.027
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs222020; hg19: chr4-72636272;