4-71755148-C-CTATTTATTTATTTATTTATT

Position:

• chr4-71755148-C-CTATTTATTTATTTATTTATT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000273951.13(GC):​c.1035-42_1035-41insAATAAATAAATAAATAAATA 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 0.0074 (7 hom., cov: 0)
  • Exomes 𝑓: 0.0021 (17 hom.)
  • Failed GnomAD Quality Control
• Consequence: GC ENST00000273951.13 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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GC	NM_000583.4	c.1035-42_1035-41insAATAAATAAATAAATAAATA		intron_variant		ENST00000273951.13	NP_000574.2
GC	NM_001204306.1	c.1035-42_1035-41insAATAAATAAATAAATAAATA		intron_variant			NP_001191235.1
GC	NM_001204307.1	c.1092-42_1092-41insAATAAATAAATAAATAAATA		intron_variant			NP_001191236.1
GC	XM_006714177.3	c.1035-42_1035-41insAATAAATAAATAAATAAATA		intron_variant			XP_006714240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000273951.13	c.1035-42_1035-41insAATAAATAAATAAATAAATA		intron_variant		1	NM_000583.4	ENSP00000273951	P1

Frequencies

GnomAD3 genomes AF: 0.00735 AC: 1067 AN: 145144 Hom.: 7 Cov.: 0

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00562

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.00873

Gnomad SAS AF: 0.00405

Gnomad FIN AF: 0.000561

Gnomad MID AF: 0.0194

Gnomad NFE AF: 0.00411

Gnomad OTH AF: 0.00803

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00215 AC: 610 AN: 284194 Hom.: 17 Cov.: 9 AF XY: 0.00241 AC XY: 380 AN XY: 157742

Gnomad4 AFR exome AF: 0.00452

Gnomad4 AMR exome AF: 0.00176

Gnomad4 ASJ exome AF: 0.0150

Gnomad4 EAS exome AF: 0.000987

Gnomad4 SAS exome AF: 0.00180

Gnomad4 FIN exome AF: 0.000697

Gnomad4 NFE exome AF: 0.00182

Gnomad4 OTH exome AF: 0.00351

GnomAD4 genome AF: 0.00736 AC: 1069 AN: 145232 Hom.: 7 Cov.: 0 AF XY: 0.00728 AC XY: 512 AN XY: 70312

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.00562

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.00875

Gnomad4 SAS AF: 0.00406

Gnomad4 FIN AF: 0.000561

Gnomad4 NFE AF: 0.00411

Gnomad4 OTH AF: 0.00795

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;