rs11573018

chr4-57110554-C-T

Variant summary

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

The ENST00000667601.1(ENSG00000287369):n.8C>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 0.119 in 151,640 control chromosomes in the GnomAD database, including 1,209 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 (1209 hom., cov: 32)
• Consequence: ENST00000667601.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP7-AS1	NR_034081.1	n.209+584C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667601.1	n.8C>T		non_coding_transcript_exon_variant	1/1
IGFBP7-AS1	ENST00000499667.6	n.209+584C>T		intron_variant, non_coding_transcript_variant		1
IGFBP7-AS1	ENST00000508328.6	n.191+584C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18004 AN: 151528 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00234

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.119 AC: 18005 AN: 151640 Hom.: 1209 Cov.: 32 AF XY: 0.121 AC XY: 8955 AN XY: 74098

Gnomad4 AFR AF: 0.0763

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.00234

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.122

Alfa AF: 0.136 Hom.: 190

Bravo AF: 0.109

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.62
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11573018; hg19: chr4-57976720;