4-71755148-CTATTTATT-C

Position:

• chr4-71755148-CTATTTATT-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000583.4(GC):​c.1035-49_1035-42delAATAAATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00057 in 429,470 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0012 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00027 (0 hom.)
• Consequence: GC NM_000583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GC	NM_000583.4	c.1035-49_1035-42delAATAAATA		intron_variant		ENST00000273951.13	NP_000574.2
GC	NM_001204307.1	c.1092-49_1092-42delAATAAATA		intron_variant			NP_001191236.1
GC	NM_001204306.1	c.1035-49_1035-42delAATAAATA		intron_variant			NP_001191235.1
GC	XM_006714177.3	c.1035-49_1035-42delAATAAATA		intron_variant			XP_006714240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000273951.13	c.1035-49_1035-42delAATAAATA		intron_variant		1	NM_000583.4	ENSP00000273951.8

Frequencies

GnomAD3 genomes AF: 0.00116 AC: 169 AN: 145154 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00406

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000347

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000300

Gnomad OTH AF: 0.00151

GnomAD4 exome AF: 0.000267 AC: 76 AN: 284228 Hom.: 0 AF XY: 0.000190 AC XY: 30 AN XY: 157762

Gnomad4 AFR exome AF: 0.00545

Gnomad4 AMR exome AF: 0.000220

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000987

Gnomad4 SAS exome AF: 0.0000601

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000106

Gnomad4 OTH exome AF: 0.000686

GnomAD4 genome AF: 0.00116 AC: 169 AN: 145242 Hom.: 1 Cov.: 0 AF XY: 0.00115 AC XY: 81 AN XY: 70318

Gnomad4 AFR AF: 0.00405

Gnomad4 AMR AF: 0.000347

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000300

Gnomad4 OTH AF: 0.00149

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;