chr5-148148686-C-T

Variant names:

• chr5-148148686-C-T
• rs1016256
• ENST00000667608.1:n.1257-54944G>A

Variant summary

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

The ENST00000667608.1(FBXO38-DT):​n.1257-54944G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,812 control chromosomes in the GnomAD database, including 12,876 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 0.38 (12876 hom., cov: 32)
• Consequence: FBXO38-DT ENST00000667608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXO38-DT	ENST00000667608.1	n.1257-54944G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58245 AN: 151694 Hom.: 12879 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.384 AC: 58244 AN: 151812 Hom.: 12876 Cov.: 32 AF XY: 0.382 AC XY: 28352 AN XY: 74182

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.403

Alfa AF: 0.489 Hom.: 15784

Bravo AF: 0.362

Asia WGS AF: 0.241 AC: 840 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1016256; hg19: chr5-147528249;