4-71755148-CTATTTATTTATT-CTATTTATT

Variant names:

• chr4-71755148-CTATT-C
• rs58603194
• NM_000583.4:c.1035-45_1035-42delAATA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_000583.4(GC):​c.1035-45_1035-42delAATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000605 in 429,452 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00092 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00045 (3 hom.)
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GC	NM_000583.4	c.1035-45_1035-42delAATA		intron_variant	Intron 8 of 12	ENST00000273951.13	NP_000574.2
GC	NM_001204307.1	c.1092-45_1092-42delAATA		intron_variant	Intron 9 of 13		NP_001191236.1
GC	NM_001204306.1	c.1035-45_1035-42delAATA		intron_variant	Intron 9 of 13		NP_001191235.1
GC	NM_001440458.1	c.1035-45_1035-42delAATA		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.1035-45_1035-42delAATA		intron_variant	Intron 8 of 12	1	NM_000583.4	ENSP00000273951.8

Frequencies

GnomAD3 genomes AF: 0.000902 AC: 131 AN: 145156 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00261

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000486

Gnomad ASJ AF: 0.000584

Gnomad EAS AF: 0.000203

Gnomad SAS AF: 0.000674

Gnomad FIN AF: 0.000112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000195

Gnomad OTH AF: 0.00100

GnomAD4 exome AF: 0.000447 AC: 127 AN: 284208 Hom.: 3 AF XY: 0.000469 AC XY: 74 AN XY: 157752

African (AFR) AF: 0.00346 AC: 26 AN: 7522

American (AMR) AF: 0.000331 AC: 3 AN: 9070

Ashkenazi Jewish (ASJ) AF: 0.00116 AC: 8 AN: 6876

East Asian (EAS) AF: 0.0000987 AC: 1 AN: 10136

South Asian (SAS) AF: 0.000661 AC: 11 AN: 16644

European-Finnish (FIN) AF: 0.000218 AC: 5 AN: 22950

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

European-Non Finnish (NFE) AF: 0.000329 AC: 65 AN: 197428

Other (OTH) AF: 0.000686 AC: 8 AN: 11664

GnomAD4 genome AF: 0.000916 AC: 133 AN: 145244 Hom.: 0 Cov.: 0 AF XY: 0.000825 AC XY: 58 AN XY: 70318

African (AFR) AF: 0.00265 AC: 104 AN: 39232

American (AMR) AF: 0.000485 AC: 7 AN: 14420

Ashkenazi Jewish (ASJ) AF: 0.000584 AC: 2 AN: 3422

East Asian (EAS) AF: 0.000204 AC: 1 AN: 4914

South Asian (SAS) AF: 0.000676 AC: 3 AN: 4436

European-Finnish (FIN) AF: 0.000112 AC: 1 AN: 8910

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.000195 AC: 13 AN: 66714

Other (OTH) AF: 0.000994 AC: 2 AN: 2012

Alfa AF: 0.000208 Hom.: 39

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.72
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs58603194; hg19: chr4-72620865;