4-57110791-C-T

Variant summary

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

The ENST00000667601.1(ENSG00000287369):n.245C>T 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 0.492 in 151,998 control chromosomes in the GnomAD database, including 19,314 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 0.49 (19314 hom., cov: 31)
• Consequence: ENST00000667601.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

Genes affected

(HGNC:):

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP7-AS1	NR_034081.1	n.209+821C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667601.1	n.245C>T		non_coding_transcript_exon_variant	1/1
IGFBP7-AS1	ENST00000499667.6	n.209+821C>T		intron_variant, non_coding_transcript_variant		1
IGFBP7-AS1	ENST00000508328.6	n.191+821C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74717 AN: 151880 Hom.: 19278 Cov.: 31

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.492 AC: 74815 AN: 151998 Hom.: 19314 Cov.: 31 AF XY: 0.496 AC XY: 36848 AN XY: 74298

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.467

Alfa AF: 0.406 Hom.: 2079

Bravo AF: 0.492

Asia WGS AF: 0.533 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.8
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075349; hg19: chr4-57976957;