rs12501656

Variant names:

• chr4-57166435-G-A
• rs12501656
• ENST00000499667.6:n.210-21735G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000499667.6(IGFBP7-AS1):​n.210-21735G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,146 control chromosomes in the GnomAD database, including 2,922 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 0.19 (2922 hom., cov: 32)
• Consequence: IGFBP7-AS1 ENST00000499667.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 1 publications found

Genes affected

IGFBP7-AS1 (HGNC:40296): (IGFBP7 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499667.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGFBP7-AS1	NR_034081.1		n.210-21735G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGFBP7-AS1	ENST00000499667.6	TSL:1	n.210-21735G>A		intron	N/A
	IGFBP7-AS1	ENST00000508328.7	TSL:3	n.231-34698G>A		intron	N/A
	IGFBP7-AS1	ENST00000777009.1		n.208-34698G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28318 AN: 152026 Hom.: 2918 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.186 AC: 28339 AN: 152146 Hom.: 2922 Cov.: 32 AF XY: 0.187 AC XY: 13888 AN XY: 74410

African (AFR) AF: 0.114 AC: 4746 AN: 41514

American (AMR) AF: 0.277 AC: 4238 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3468

East Asian (EAS) AF: 0.108 AC: 558 AN: 5164

South Asian (SAS) AF: 0.126 AC: 606 AN: 4822

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14911 AN: 67978

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.174 Hom.: 372

Bravo AF: 0.193

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.42
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs12501656; hg19: chr4-58032601;