6-1607368-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 6-1607368-C-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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXCUT	NR_125804.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXCUT	ENST00000652712.1			downstream_gene_variant

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

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.108

Alfa AF: 0.107 Hom.: 1341

Bravo AF: 0.0943

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.6
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2235718; hg19: chr6-1607603;