Variant chr4-57110400-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000499667.6(IGFBP7-AS1):n.209+430C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,249,564 control chromosomes in the GnomAD database, including 9,567 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 2500 hom., cov: 32)

Exomes 𝑓: 0.096 ( 7067 hom. )

Consequence

IGFBP7-AS1
ENST00000499667.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.96

Variant links:

Genes affected

IGFBP7-AS1 (HGNC:):

IGFBP7-AS1 links:

IGFBP7 (HGNC:5476): (insulin like growth factor binding protein 7) This gene encodes a member of the insulin-like growth factor (IGF)-binding protein (IGFBP) family. IGFBPs bind IGFs with high affinity, and regulate IGF availability in body fluids and tissues and modulate IGF binding to its receptors. This protein binds IGF-I and IGF-II with relatively low affinity, and belongs to a subfamily of low-affinity IGFBPs. It also stimulates prostacyclin production and cell adhesion. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and one variant has been associated with retinal arterial macroaneurysm (PMID:21835307). [provided by RefSeq, Dec 2011]

IGFBP7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
IGFBP7-AS1	NR_034081.1 linkuse as main transcript	n.209+430C>A	intron_variant
IGFBP7	NM_001553.3 linkuse as main transcript	c.-49G>T	upstream_gene_variant	ENST00000295666.6	NP_001544.1	Q16270-1
IGFBP7	NM_001253835.2 linkuse as main transcript	c.-49G>T	upstream_gene_variant		NP_001240764.1	Q16270-2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
IGFBP7-AS1	ENST00000499667.6 linkuse as main transcript	n.209+430C>A	intron_variant	1
IGFBP7-AS1	ENST00000508328.6 linkuse as main transcript	n.191+430C>A	intron_variant	3
IGFBP7	ENST00000295666.6 linkuse as main transcript	c.-49G>T	upstream_gene_variant	1	NM_001553.3	ENSP00000295666.4	Q16270-1
IGFBP7	ENST00000514062.2 linkuse as main transcript	c.-49G>T	upstream_gene_variant	2		ENSP00000486293.1	Q16270-2

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23200

AN:

151194

Hom.:

2501

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.0865

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.0707

Gnomad MID

AF:

0.137

Gnomad NFE

AF:

0.0797

Gnomad OTH

AF:

0.136

GnomAD3 exomes

AF:

0.374

AC:

119

AN:

318

Hom.:

AF XY:

0.342

AC XY:

AN XY:

202

show subpopulations

Gnomad AFR exome

AF:

0.674

Gnomad AMR exome

AF:

0.438

Gnomad ASJ exome

AF:

0.500

Gnomad EAS exome

AF:

0.500

Gnomad SAS exome

AF:

0.321

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.240

Gnomad OTH exome

AF:

0.500

GnomAD4 exome

AF:

0.0956

AC:

105000

AN:

1098262

Hom.:

7067

Cov.:

AF XY:

0.0959

AC XY:

50335

AN XY:

524888

show subpopulations

Gnomad4 AFR exome

AF:

0.310

Gnomad4 AMR exome

AF:

0.150

Gnomad4 ASJ exome

AF:

0.100

Gnomad4 EAS exome

AF:

0.392

Gnomad4 SAS exome

AF:

0.128

Gnomad4 FIN exome

AF:

0.0718

Gnomad4 NFE exome

AF:

0.0807

Gnomad4 OTH exome

AF:

0.113

GnomAD4 genome

AF:

0.154

AC:

23226

AN:

151302

Hom.:

2500

Cov.:

AF XY:

0.154

AC XY:

11360

AN XY:

73942

show subpopulations

Gnomad4 AFR

AF:

0.287

Gnomad4 AMR

AF:

0.136

Gnomad4 ASJ

AF:

0.0865

Gnomad4 EAS

AF:

0.347

Gnomad4 SAS

AF:

0.130

Gnomad4 FIN

AF:

0.0707

Gnomad4 NFE

AF:

0.0797

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.0345

Hom.:

Bravo

AF:

0.168

Asia WGS

AF:

0.198

AC:

657

AN:

3324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.38

DANN

Benign

0.86

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over