6-1598707-C-T

Variant names:

• chr6-1598707-C-T
• rs2235715
• ENST00000841110.1:n.150+5190C>T

Variant summary

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

The ENST00000841110.1(FOXCUT):​n.150+5190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,258 control chromosomes in the GnomAD database, including 2,221 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 0.15 (2221 hom., cov: 33)
• Consequence: FOXCUT ENST00000841110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXCUT	ENST00000841110.1	n.150+5190C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22551 AN: 152140 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.148 AC: 22582 AN: 152258 Hom.: 2221 Cov.: 33 AF XY: 0.153 AC XY: 11421 AN XY: 74448

African (AFR) AF: 0.0476 AC: 1977 AN: 41572

American (AMR) AF: 0.294 AC: 4507 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1009 AN: 5160

South Asian (SAS) AF: 0.165 AC: 799 AN: 4830

European-Finnish (FIN) AF: 0.190 AC: 2012 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10874 AN: 68008

Other (OTH) AF: 0.181 AC: 383 AN: 2114

Alfa AF: 0.163 Hom.: 4803

Bravo AF: 0.157

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs2235715; hg19: chr6-1598942;