chr5-148291690-A-G

Variant names:

• chr5-148291690-A-G
• rs10515607
• ENST00000501695.4:n.677-695T>C

Variant summary

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

The ENST00000501695.4(FBXO38-DT):​n.677-695T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,194 control chromosomes in the GnomAD database, including 1,078 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 0.066 (1078 hom., cov: 32)
• Consequence: FBXO38-DT ENST00000501695.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 0 publications found

Genes affected

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

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 (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXO38-DT	NR_105057.1	n.659-695T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXO38-DT	ENST00000501695.4	n.677-695T>C		intron_variant	Intron 3 of 4	2
FBXO38-DT	ENST00000648571.1	n.372-695T>C		intron_variant	Intron 3 of 5
FBXO38-DT	ENST00000657331.1	n.680-695T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10001 AN: 152076 Hom.: 1074 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00215

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0658 AC: 10018 AN: 152194 Hom.: 1078 Cov.: 32 AF XY: 0.0634 AC XY: 4719 AN XY: 74428

African (AFR) AF: 0.226 AC: 9352 AN: 41462

American (AMR) AF: 0.0229 AC: 350 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4830

European-Finnish (FIN) AF: 0.000565 AC: 6 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00215 AC: 146 AN: 68024

Other (OTH) AF: 0.0497 AC: 105 AN: 2114

Alfa AF: 0.0368 Hom.: 155

Bravo AF: 0.0744

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.79
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs10515607; hg19: chr5-147671253;