4-71755148-C-CTATT

Position:

• chr4-71755148-C-CTATT

Variant summary

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

The NM_000583.4(GC):​c.1035-45_1035-42dupAATA 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 0.032 (113 hom., cov: 0)
  • Exomes 𝑓: 0.026 (191 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 (AFR) allele frequency at 95% confidence interval = 0.0571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GC	NM_000583.4	c.1035-45_1035-42dupAATA		intron_variant		ENST00000273951.13	NP_000574.2
GC	NM_001204307.1	c.1092-45_1092-42dupAATA		intron_variant			NP_001191236.1
GC	NM_001204306.1	c.1035-45_1035-42dupAATA		intron_variant			NP_001191235.1
GC	XM_006714177.3	c.1035-45_1035-42dupAATA		intron_variant			XP_006714240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000273951.13	c.1035-45_1035-42dupAATA		intron_variant		1	NM_000583.4	ENSP00000273951.8

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4590 AN: 145118 Hom.: 114 Cov.: 0

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.0536

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0105

Gnomad EAS AF: 0.000609

Gnomad SAS AF: 0.00787

Gnomad FIN AF: 0.00864

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0336

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0261 AC: 7298 AN: 279600 Hom.: 191 Cov.: 9 AF XY: 0.0250 AC XY: 3876 AN XY: 155040

Gnomad4 AFR exome AF: 0.0478

Gnomad4 AMR exome AF: 0.0137

Gnomad4 ASJ exome AF: 0.0110

Gnomad4 EAS exome AF: 0.00109

Gnomad4 SAS exome AF: 0.00935

Gnomad4 FIN exome AF: 0.00808

Gnomad4 NFE exome AF: 0.0313

Gnomad4 OTH exome AF: 0.0263

GnomAD4 genome AF: 0.0317 AC: 4599 AN: 145206 Hom.: 113 Cov.: 0 AF XY: 0.0314 AC XY: 2205 AN XY: 70294

Gnomad4 AFR AF: 0.0591

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0105

Gnomad4 EAS AF: 0.000611

Gnomad4 SAS AF: 0.00789

Gnomad4 FIN AF: 0.00864

Gnomad4 NFE AF: 0.0254

Gnomad4 OTH AF: 0.0333

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;