rs11573014

Variant names:

• chr4-57111075-C-G
• rs11573014
• ENST00000499667.6:n.209+1105C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ENSG00000287369 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667601.1. 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.209+1105C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGFBP7-AS1	ENST00000499667.6	TSL:1	n.209+1105C>G		intron	N/A
	ENSG00000287369	ENST00000667601.1		n.529C>G		non_coding_transcript_exon	Exon 1 of 1
	IGFBP7-AS1	ENST00000508328.7	TSL:3	n.230+1105C>G		intron	N/A

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

African (AFR) AF: 0.0765 AC: 3178 AN: 41540

American (AMR) AF: 0.0969 AC: 1482 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5172

South Asian (SAS) AF: 0.0607 AC: 292 AN: 4814

European-Finnish (FIN) AF: 0.214 AC: 2263 AN: 10592

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10006 AN: 68004

Other (OTH) AF: 0.125 AC: 263 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.49
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11573014;

hg19: chr4-57977241;

COSMIC: COSV55271893;