4-71755148-C-CTATTTATTTATT

Position:

• chr4-71755148-C-CTATTTATTTATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000583.4(GC):​c.1035-53_1035-42dupAATAAATAAATA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (1864 hom., cov: 0)
  • Exomes 𝑓: 0.078 (1902 hom.)
  • Failed GnomAD Quality Control
• Consequence: GC NM_000583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

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]

GC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GC	NM_000583.4	c.1035-53_1035-42dupAATAAATAAATA		intron_variant		ENST00000273951.13	NP_000574.2
GC	NM_001204307.1	c.1092-53_1092-42dupAATAAATAAATA		intron_variant			NP_001191236.1
GC	NM_001204306.1	c.1035-53_1035-42dupAATAAATAAATA		intron_variant			NP_001191235.1
GC	XM_006714177.3	c.1035-53_1035-42dupAATAAATAAATA		intron_variant			XP_006714240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000273951.13	c.1035-53_1035-42dupAATAAATAAATA		intron_variant		1	NM_000583.4	ENSP00000273951.8

Frequencies

GnomAD3 genomes AF: 0.149 AC: 21625 AN: 144960 Hom.: 1860 Cov.: 0

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0814

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.116

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.137

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0781 AC: 22110 AN: 283204 Hom.: 1902 Cov.: 9 AF XY: 0.0814 AC XY: 12793 AN XY: 157196

Gnomad4 AFR exome AF: 0.0898

Gnomad4 AMR exome AF: 0.0593

Gnomad4 ASJ exome AF: 0.0587

Gnomad4 EAS exome AF: 0.177

Gnomad4 SAS exome AF: 0.0809

Gnomad4 FIN exome AF: 0.0676

Gnomad4 NFE exome AF: 0.0745

Gnomad4 OTH exome AF: 0.0917

GnomAD4 genome AF: 0.149 AC: 21637 AN: 145048 Hom.: 1864 Cov.: 0 AF XY: 0.149 AC XY: 10466 AN XY: 70228

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0814

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58603194; hg19: chr4-72620865;