rs12501656

Positions:

• chr4-57166435-G-A

Variant summary

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

The NR_034081.1(IGFBP7-AS1):​n.210-21735G>A variant causes a intron, non coding transcript 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 NR_034081.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP7-AS1	NR_034081.1	n.210-21735G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGFBP7-AS1	ENST00000499667.6	n.210-21735G>A		intron_variant, non_coding_transcript_variant		1
IGFBP7-AS1	ENST00000508328.6	n.192-34698G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.201

Alfa AF: 0.176 Hom.: 367

Bravo AF: 0.193

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12501656; hg19: chr4-58032601;