rs7709159

Positions:

• chr5-148296273-C-T

Variant summary

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

The NR_105057.1(FBXO38-DT):​n.659-5278G>A 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 0.193 in 152,150 control chromosomes in the GnomAD database, including 7,949 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 0.19 (7949 hom., cov: 32)
• Consequence: FBXO38-DT NR_105057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBXO38-DT	NR_105057.1	n.659-5278G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBXO38-DT	ENST00000667608.1	n.516-31646G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29256 AN: 152032 Hom.: 7906 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00720

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.193 AC: 29370 AN: 152150 Hom.: 7949 Cov.: 32 AF XY: 0.191 AC XY: 14173 AN XY: 74372

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.0885

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.0320

Gnomad4 NFE AF: 0.00720

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0547 Hom.: 813

Bravo AF: 0.217

Asia WGS AF: 0.204 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.88
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7709159; hg19: chr5-147675836;