chr4-71755148-CTATTTATTTATT-C

Variant names:

• chr4-71755148-CTATTTATTTATT-C
• rs58603194
• NM_000583.4:c.1035-53_1035-42delAATAAATAAATA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000583.4(GC):​c.1035-53_1035-42delAATAAATAAATA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000014 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GC NM_000583.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GC	NM_000583.4	c.1035-53_1035-42delAATAAATAAATA		intron_variant	Intron 8 of 12	ENST00000273951.13	NP_000574.2
GC	NM_001204307.1	c.1092-53_1092-42delAATAAATAAATA		intron_variant	Intron 9 of 13		NP_001191236.1
GC	NM_001204306.1	c.1035-53_1035-42delAATAAATAAATA		intron_variant	Intron 9 of 13		NP_001191235.1
GC	NM_001440458.1	c.1035-53_1035-42delAATAAATAAATA		intron_variant	Intron 8 of 11		NP_001427387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GC	ENST00000273951.13	c.1035-53_1035-42delAATAAATAAATA		intron_variant	Intron 8 of 12	1	NM_000583.4	ENSP00000273951.8

Frequencies

GnomAD3 genomes AF: 0.0000138 AC: 2 AN: 145156 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000511

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 284228 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 157762

African (AFR) AF: 0.00 AC: 0 AN: 7528

American (AMR) AF: 0.00 AC: 0 AN: 9072

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6876

East Asian (EAS) AF: 0.00 AC: 0 AN: 10136

South Asian (SAS) AF: 0.00 AC: 0 AN: 16644

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22950

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1918

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 197438

Other (OTH) AF: 0.00 AC: 0 AN: 11666

GnomAD4 genome AF: 0.0000138 AC: 2 AN: 145156 Hom.: 0 Cov.: 0 AF XY: 0.0000142 AC XY: 1 AN XY: 70220

African (AFR) AF: 0.0000511 AC: 2 AN: 39124

American (AMR) AF: 0.00 AC: 0 AN: 14402

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3422

East Asian (EAS) AF: 0.00 AC: 0 AN: 4928

South Asian (SAS) AF: 0.00 AC: 0 AN: 4448

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8910

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 310

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66724

Other (OTH) AF: 0.00 AC: 0 AN: 1992

Alfa AF: 0.00 Hom.: 39

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs58603194; hg19: chr4-72620865;