rs3802122

chr7-157179604-T-Achr7-157179604-T-C

Variant summary

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

The NM_014671.3(UBE3C):c.616+757T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,988 control chromosomes in the GnomAD database, including 10,371 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 0.34 (10371 hom., cov: 32)
• Consequence: UBE3C NM_014671.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612

Genes affected

UBE3C (HGNC:16803): (ubiquitin protein ligase E3C) Enables ubiquitin protein ligase activity. Involved in protein polyubiquitination. Predicted to be located in nucleus. Predicted to be part of proteasome complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE3C	NM_014671.3	c.616+757T>A		intron_variant		ENST00000348165.10
UBE3C	XM_005249564.5	c.541+757T>A		intron_variant
UBE3C	XM_047421072.1	c.553+757T>A		intron_variant
UBE3C	XM_047421073.1	c.616+757T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE3C	ENST00000348165.10	c.616+757T>A		intron_variant		1	NM_014671.3	P1
UBE3C	ENST00000389103.4	c.487+757T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52385 AN: 151870 Hom.: 10361 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.345 AC: 52430 AN: 151988 Hom.: 10371 Cov.: 32 AF XY: 0.348 AC XY: 25829 AN XY: 74288

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.333

Alfa AF: 0.135 Hom.: 216

Bravo AF: 0.365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.5
Dann	Benign	0.84

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: rs3802122; hg19: chr7-156972298;