ENST00000652712.1:n.1593T>C

Variant names:

• chr6-1606881-T-C
• rs2235716
• ENST00000652712.1:n.1593T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652712.1(FOXCUT):​n.1593T>C 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 0.406 in 152,150 control chromosomes in the GnomAD database, including 13,293 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 0.41 (13293 hom., cov: 33)
• Consequence: FOXCUT ENST00000652712.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

Genes affected

FOXCUT (HGNC:50650): (FOXC1 upstream transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652712.1. 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
	FOXCUT	NR_125804.1		n.1135T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXCUT	ENST00000652712.1		n.1593T>C		non_coding_transcript_exon	Exon 2 of 2
	FOXCUT	ENST00000841111.1		n.1748T>C		non_coding_transcript_exon	Exon 2 of 2
	FOXCUT	ENST00000841113.1		n.*19T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61616 AN: 152030 Hom.: 13257 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.406 AC: 61714 AN: 152150 Hom.: 13293 Cov.: 33 AF XY: 0.408 AC XY: 30339 AN XY: 74410

African (AFR) AF: 0.506 AC: 21001 AN: 41478

American (AMR) AF: 0.514 AC: 7858 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1227 AN: 3472

East Asian (EAS) AF: 0.644 AC: 3328 AN: 5168

South Asian (SAS) AF: 0.349 AC: 1685 AN: 4822

European-Finnish (FIN) AF: 0.323 AC: 3421 AN: 10590

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21882 AN: 68006

Other (OTH) AF: 0.409 AC: 864 AN: 2114

Alfa AF: 0.379 Hom.: 3976

Bravo AF: 0.430

Asia WGS AF: 0.487 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.19
DANN	Benign	0.68
PhyloP100		-1.4

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: rs2235716;

hg19: chr6-1607116;