6-1607368-C-T

Variant names:

• chr6-1607368-C-T
• rs2235718
• ENST00000652712.1:n.*14C>T

Variant summary

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

The NR_125804.1(FOXCUT):​n.*10C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,238 control chromosomes in the GnomAD database, including 976 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 0.10 (976 hom., cov: 33)
• Consequence: FOXCUT NR_125804.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125804.1. 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.*10C>T		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXCUT	ENST00000652712.1		n.*14C>T		downstream_gene	N/A
	FOXCUT	ENST00000841111.1		n.*10C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15404 AN: 152120 Hom.: 979 Cov.: 33

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.101 AC: 15393 AN: 152238 Hom.: 976 Cov.: 33 AF XY: 0.105 AC XY: 7817 AN XY: 74432

African (AFR) AF: 0.0541 AC: 2249 AN: 41538

American (AMR) AF: 0.0807 AC: 1234 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1256 AN: 5178

South Asian (SAS) AF: 0.222 AC: 1072 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1366 AN: 10594

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7270 AN: 68018

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.104 Hom.: 1608

Bravo AF: 0.0943

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.29
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2235718; hg19: chr6-1607603;