rs4714468

Variant names:

• chr6-41485258-G-A
• rs4714468
• ENST00000691406.2:n.243+1807C>T

Variant summary

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

The ENST00000691406.2(FOXP4-AS1):​n.243+1807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,212 control chromosomes in the GnomAD database, including 1,420 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 0.12 (1420 hom., cov: 32)
• Consequence: FOXP4-AS1 ENST00000691406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 2 publications found

Genes affected

FOXP4-AS1 (HGNC:50332): (FOXP4 antisense RNA 1)

LOC112267957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691406.2. 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
	FOXP4-AS1	ENST00000691406.2		n.243+1807C>T		intron	N/A
	FOXP4-AS1	ENST00000727791.1		n.381+1807C>T		intron	N/A
	FOXP4-AS1	ENST00000727792.1		n.225+1807C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18354 AN: 152094 Hom.: 1419 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.121 AC: 18365 AN: 152212 Hom.: 1420 Cov.: 32 AF XY: 0.127 AC XY: 9456 AN XY: 74388

African (AFR) AF: 0.0505 AC: 2100 AN: 41550

American (AMR) AF: 0.192 AC: 2937 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5182

South Asian (SAS) AF: 0.282 AC: 1358 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1849 AN: 10572

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8189 AN: 68024

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.119 Hom.: 2797

Bravo AF: 0.118

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.96
DANN	Benign	0.94
PhyloP100		-0.39

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: rs4714468;

hg19: chr6-41452996;