rs17630266

Variant names:

• chr13-40619895-G-A
• rs17630266
• NM_002015.4:c.630+45688C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-40619895-G-A
• chr13-40619895-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002015.4(FOXO1):​c.630+45688C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: FOXO1 NM_002015.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.27
• Publications: 8 publications found

Genes affected

FOXO1 (HGNC:3819): (forkhead box O1) This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in myogenic growth and differentiation. Translocation of this gene with PAX3 has been associated with alveolar rhabdomyosarcoma. [provided by RefSeq, Jul 2008]

RLIMP1 (HGNC:39682): (ring finger protein, LIM domain interacting pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXO1	NM_002015.4	c.630+45688C>T		intron_variant	Intron 1 of 2	ENST00000379561.6	NP_002006.2
RLIMP1		n.40619895G>A		intragenic_variant
FOXO1	XM_011535008.3	c.-5659C>T		5_prime_UTR_variant	Exon 1 of 3		XP_011533310.1
FOXO1	XM_047430204.1	c.-82+25444C>T		intron_variant	Intron 1 of 2		XP_047286160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXO1	ENST00000379561.6	c.630+45688C>T		intron_variant	Intron 1 of 2	1	NM_002015.4	ENSP00000368880.4
RLIMP1	ENST00000339626.5	n.833G>A		non_coding_transcript_exon_variant	Exon 2 of 3	6
FOXO1	ENST00000655267.1	n.333+45688C>T		intron_variant	Intron 1 of 2
FOXO1	ENST00000660760.1	n.397+13252C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 4

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.8
DANN	Benign	0.57
PhyloP100		3.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs17630266; hg19: chr13-41194032;