rs1432689

Positions:

• chr5-148198699-T-C
• chr5-148198699-T-G

Variant summary

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

The ENST00000667608.1(FBXO38-DT):​n.1256+65188A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,912 control chromosomes in the GnomAD database, including 16,886 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 0.46 (16886 hom., cov: 32)
• Consequence: FBXO38-DT ENST00000667608.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

FBXO38-DT (HGNC:55589): (FBXO38 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXO38-DT	ENST00000667608.1	n.1256+65188A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70025 AN: 151794 Hom.: 16864 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.461 AC: 70070 AN: 151912 Hom.: 16886 Cov.: 32 AF XY: 0.466 AC XY: 34571 AN XY: 74222

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.459

Alfa AF: 0.464 Hom.: 26429

Bravo AF: 0.464

Asia WGS AF: 0.616 AC: 2136 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1432689; hg19: chr5-147578262; COSMIC: COSV100347234;