rs11573014

Positions:

• chr4-57111075-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667601.1(ENSG00000287369):​n.529C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,208 control chromosomes in the GnomAD database, including 1,220 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 0.12 (1220 hom., cov: 32)
• Consequence: ENSG00000287369 ENST00000667601.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

IGFBP7-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGFBP7-AS1	NR_034081.1	n.209+1105C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGFBP7-AS1	ENST00000499667.6	n.209+1105C>G		intron_variant		1
ENSG00000287369	ENST00000667601.1	n.529C>G		non_coding_transcript_exon_variant	1/1
IGFBP7-AS1	ENST00000508328.6	n.191+1105C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18177 AN: 152090 Hom.: 1220 Cov.: 32

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.126

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.119 AC: 18178 AN: 152208 Hom.: 1220 Cov.: 32 AF XY: 0.121 AC XY: 9031 AN XY: 74394

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.125

Alfa AF: 0.137 Hom.: 191

Bravo AF: 0.109

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11573014; hg19: chr4-57977241; COSMIC: COSV55271893;