rs1432689

Variant names:

• chr5-148198699-T-C
• rs1432689
• ENST00000667608.1:n.1256+65188A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000667608.1(FBXO38-DT):​n.1256+65188A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXO38-DT	ENST00000667608.1		n.1256+65188A>G		intron	N/A

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

African (AFR) AF: 0.364 AC: 15074 AN: 41422

American (AMR) AF: 0.547 AC: 8349 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3468

East Asian (EAS) AF: 0.719 AC: 3705 AN: 5154

South Asian (SAS) AF: 0.511 AC: 2459 AN: 4816

European-Finnish (FIN) AF: 0.505 AC: 5323 AN: 10544

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32227 AN: 67928

Other (OTH) AF: 0.459 AC: 971 AN: 2114

Alfa AF: 0.463 Hom.: 41066

Bravo AF: 0.464

Asia WGS AF: 0.616 AC: 2136 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.67
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1432689;

hg19: chr5-147578262;

COSMIC: COSV100347234;