chr1-47416235-T-TG

Position:

• chr1-47416235-T-TG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NR_126355.1(LINC01389):​n.29-6335_29-6334insC 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 0.0224 in 934,374 control chromosomes in the GnomAD database, including 404 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.045 (296 hom., cov: 31)
  • Exomes 𝑓: 0.018 (108 hom.)
• Consequence: LINC01389 NR_126355.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.312

Genes affected

LINC01389 (HGNC:):

FOXE3 (HGNC:3808): (forkhead box E3) This intronless gene belongs to the forkhead family of transcription factors, which is characterized by a distinct forkhead domain. The protein encoded functions as a lens-specific transcription factor and plays an important role in vertebrate lens formation. Mutations in this gene are associated with anterior segment mesenchymal dysgenesis and congenital primary aphakia. [provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-47416235-T-TG is Benign according to our data. Variant chr1-47416235-T-TG is described in ClinVar as [Benign]. Clinvar id is 1228957.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01389	NR_126355.1	n.29-6335_29-6334insC		intron_variant, non_coding_transcript_variant
FOXE3	NM_012186.3			upstream_gene_variant		ENST00000335071.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXE3	ENST00000335071.4			upstream_gene_variant			NM_012186.3	P1

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6434 AN: 142578 Hom.: 295 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00116

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0178

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.00515

Gnomad MID AF: 0.0400

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0382

GnomAD4 exome AF: 0.0183 AC: 14477 AN: 791726 Hom.: 108 Cov.: 12 AF XY: 0.0179 AC XY: 6793 AN XY: 378650

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.0278

Gnomad4 ASJ exome AF: 0.0259

Gnomad4 EAS exome AF: 0.144

Gnomad4 SAS exome AF: 0.0159

Gnomad4 FIN exome AF: 0.0116

Gnomad4 NFE exome AF: 0.0128

Gnomad4 OTH exome AF: 0.0264

GnomAD4 genome AF: 0.0451 AC: 6437 AN: 142648 Hom.: 296 Cov.: 31 AF XY: 0.0444 AC XY: 3084 AN XY: 69454

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.0178

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.00515

Gnomad4 NFE AF: 0.0114

Gnomad4 OTH AF: 0.0369

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 06, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs137862650; hg19: chr1-47881907;