chr16-55326137-A-AAAAGCGT

Variant names:

• chr16-55326137-A-AAAAGCGT
• rs2067217
• NM_024335.3:c.46-199_46-198insAAAGCGT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024335.3(IRX6):​c.46-199_46-198insAAAGCGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IRX6 NM_024335.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 2 publications found

Genes affected

IRX6 (HGNC:14675): (iroquois homeobox 6) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell development; neuron differentiation; and regulation of transcription, DNA-templated. Predicted to act upstream of or within detection of visible light; negative regulation of transcription, DNA-templated; and retina morphogenesis in camera-type eye. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000259283 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRX6	NM_024335.3	c.46-199_46-198insAAAGCGT		intron_variant	Intron 1 of 5	ENST00000290552.8	NP_077311.2
IRX6	XM_005256137.4	c.46-199_46-198insAAAGCGT		intron_variant	Intron 1 of 5		XP_005256194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRX6	ENST00000290552.8	c.46-199_46-198insAAAGCGT		intron_variant	Intron 1 of 5	1	NM_024335.3	ENSP00000290552.8
IRX6	ENST00000558315.1	n.211+127_211+128insAAAGCGT		intron_variant	Intron 1 of 4	1
ENSG00000259283	ENST00000558730.2	n.88+7363_88+7364insACGCTTT		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.00000661 AC: 1 AN: 151248 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000148

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 444116 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 231828

African (AFR) AF: 0.00 AC: 0 AN: 12446

American (AMR) AF: 0.00 AC: 0 AN: 15918

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13544

East Asian (EAS) AF: 0.00 AC: 0 AN: 30058

South Asian (SAS) AF: 0.00 AC: 0 AN: 42540

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29318

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1934

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 272802

Other (OTH) AF: 0.00 AC: 0 AN: 25556

GnomAD4 genome AF: 0.00000661 AC: 1 AN: 151248 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 73802

African (AFR) AF: 0.00 AC: 0 AN: 41152

American (AMR) AF: 0.00 AC: 0 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3454

East Asian (EAS) AF: 0.00 AC: 0 AN: 5114

South Asian (SAS) AF: 0.00 AC: 0 AN: 4806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10528

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.0000148 AC: 1 AN: 67692

Other (OTH) AF: 0.00 AC: 0 AN: 2074

Alfa AF: 0.00 Hom.: 1849

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs2067217; hg19: chr16-55360049;