10-101524313-T-G

Variant names:

• chr10-101524313-T-G
• rs10509750
• NM_033637.4:c.557-1700T>G

Variant summary

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

The NM_033637.4(BTRC):​c.557-1700T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 152,296 control chromosomes in the GnomAD database, including 57 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 0.020 (57 hom., cov: 32)
• Consequence: BTRC NM_033637.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

BTRC (HGNC:1144): (beta-transducin repeat containing E3 ubiquitin protein ligase) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbws class; in addition to an F-box, this protein contains multiple WD-40 repeats. The encoded protein mediates degradation of CD4 via its interaction with HIV-1 Vpu. It has also been shown to ubiquitinate phosphorylated NFKBIA (nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha), targeting it for degradation and thus activating nuclear factor kappa-B. Alternatively spliced transcript variants have been described. A related pseudogene exists in chromosome 6. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTRC	NM_033637.4	c.557-1700T>G		intron_variant	Intron 5 of 14	ENST00000370187.8	NP_378663.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTRC	ENST00000370187.8	c.557-1700T>G		intron_variant	Intron 5 of 14	1	NM_033637.4	ENSP00000359206.3

Frequencies

GnomAD3 genomes AF: 0.0197 AC: 3001 AN: 152178 Hom.: 56 Cov.: 32

Gnomad AFR AF: 0.00516

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.00663

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0197 AC: 3000 AN: 152296 Hom.: 57 Cov.: 32 AF XY: 0.0187 AC XY: 1395 AN XY: 74462

Gnomad4 AFR AF: 0.00515

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.00519

Gnomad4 EAS AF: 0.0903

Gnomad4 SAS AF: 0.00685

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0151

Alfa AF: 0.0232 Hom.: 24

Bravo AF: 0.0213

Asia WGS AF: 0.0370 AC: 127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509750; hg19: chr10-103284070;