rs222020

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000273951.13(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
ENST00000273951.13 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0270
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
GCNM_000583.4 linkuse as main transcriptc.59-1155G>A intron_variant ENST00000273951.13 NP_000574.2
GCNM_001204306.1 linkuse as main transcriptc.59-1155G>A intron_variant NP_001191235.1
GCNM_001204307.1 linkuse as main transcriptc.116-1155G>A intron_variant NP_001191236.1
GCXM_006714177.3 linkuse as main transcriptc.59-1155G>A intron_variant XP_006714240.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GCENST00000273951.13 linkuse as main transcriptc.59-1155G>A intron_variant 1 NM_000583.4 ENSP00000273951 P1P02774-1

Frequencies

GnomAD3 genomes
AF:
0.727
AC:
110277
AN:
151754
Hom.:
42341
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.457
Gnomad4 AMR
AF:
0.808
Gnomad4 ASJ
AF:
0.904
Gnomad4 EAS
AF:
0.601
Gnomad4 SAS
AF:
0.854
Gnomad4 FIN
AF:
0.796
Gnomad4 NFE
AF:
0.850
Gnomad4 OTH
AF:
0.760
Alfa
AF:
0.826
Hom.:
76455
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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs222020; hg19: chr4-72636272; API