rs7788807

Variant names:

• chr7-4728407-T-C
• rs7788807
• NM_001037165.2:c.561-12431T>C

Variant summary

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

The NM_001037165.2(FOXK1):​c.561-12431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 152,264 control chromosomes in the GnomAD database, including 631 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 0.081 (631 hom., cov: 32)
• Consequence: FOXK1 NM_001037165.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

Genes affected

FOXK1 (HGNC:23480): (forkhead box K1) Enables 14-3-3 protein binding activity; DNA-binding transcription repressor activity, RNA polymerase II-specific; and transcription cis-regulatory region binding activity. Involved in several processes, including cellular glucose homeostasis; negative regulation of autophagy; and regulation of transcription, DNA-templated. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000287665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXK1	NM_001037165.2	c.561-12431T>C		intron_variant	Intron 1 of 8	ENST00000328914.5	NP_001032242.1
LOC124901581	XR_007060199.1	n.5130T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXK1	ENST00000328914.5	c.561-12431T>C		intron_variant	Intron 1 of 8	2	NM_001037165.2	ENSP00000328720.4
ENSG00000287665	ENST00000658333.1	n.2175T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0812 AC: 12353 AN: 152146 Hom.: 623 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0345

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.0942

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

GnomAD4 genome AF: 0.0814 AC: 12393 AN: 152264 Hom.: 631 Cov.: 32 AF XY: 0.0791 AC XY: 5889 AN XY: 74458

African (AFR) AF: 0.141 AC: 5870 AN: 41534

American (AMR) AF: 0.0715 AC: 1094 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4830

European-Finnish (FIN) AF: 0.0378 AC: 401 AN: 10616

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0615 AC: 4182 AN: 68018

Other (OTH) AF: 0.0918 AC: 194 AN: 2114

Alfa AF: 0.0684 Hom.: 779

Bravo AF: 0.0895

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.39
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7788807; hg19: chr7-4768038;