rs1016256

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000309693 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667608.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXO38-DT	ENST00000667608.1		n.1257-54944G>A		intron	N/A
	ENSG00000309693	ENST00000843063.1		n.139+883C>T		intron	N/A
	ENSG00000309693	ENST00000843064.1		n.106+883C>T		intron	N/A

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

African (AFR) AF: 0.191 AC: 7923 AN: 41466

American (AMR) AF: 0.363 AC: 5524 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3466

East Asian (EAS) AF: 0.0997 AC: 513 AN: 5148

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4816

European-Finnish (FIN) AF: 0.490 AC: 5171 AN: 10544

Middle Eastern (MID) AF: 0.545 AC: 157 AN: 288

European-Non Finnish (NFE) AF: 0.501 AC: 33965 AN: 67858

Other (OTH) AF: 0.403 AC: 849 AN: 2108

Alfa AF: 0.482 Hom.: 17866

Bravo AF: 0.362

Asia WGS AF: 0.241 AC: 840 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.58
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1016256; hg19: chr5-147528249; COSMIC: COSV107163696;