6-1603452-G-C

Variant names:

• chr6-1603452-G-C
• rs2569889
• ENST00000652712.1:n.727+1072G>C

Variant summary

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

The ENST00000652712.1(FOXCUT):​n.727+1072G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,966 control chromosomes in the GnomAD database, including 23,929 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 0.56 (23929 hom., cov: 32)
• Consequence: FOXCUT ENST00000652712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXCUT	ENST00000652712.1		n.727+1072G>C		intron	N/A
	FOXCUT	ENST00000841110.1		n.151-2564G>C		intron	N/A
	FOXCUT	ENST00000841111.1		n.882+914G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84396 AN: 151848 Hom.: 23906 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.556 AC: 84474 AN: 151966 Hom.: 23929 Cov.: 32 AF XY: 0.561 AC XY: 41636 AN XY: 74272

African (AFR) AF: 0.549 AC: 22740 AN: 41400

American (AMR) AF: 0.600 AC: 9160 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4493 AN: 5180

South Asian (SAS) AF: 0.700 AC: 3357 AN: 4798

European-Finnish (FIN) AF: 0.501 AC: 5295 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35723 AN: 67964

Other (OTH) AF: 0.557 AC: 1174 AN: 2108

Alfa AF: 0.531 Hom.: 2694

Bravo AF: 0.564

Asia WGS AF: 0.791 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-0.12

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: rs2569889;

hg19: chr6-1603687;