rs6979947

Positions:

• chr7-157213169-A-G
• chr7-157213169-A-T

Variant summary

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

The NM_014671.3(UBE3C):​c.1810-3698A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,184 control chromosomes in the GnomAD database, including 16,056 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 0.41 (16056 hom., cov: 33)
• Consequence: UBE3C NM_014671.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE3C	NM_014671.3	c.1810-3698A>G		intron_variant		ENST00000348165.10	NP_055486.2
UBE3C	XM_005249564.5	c.1735-3698A>G		intron_variant			XP_005249621.1
UBE3C	XM_047421072.1	c.1747-3698A>G		intron_variant			XP_047277028.1
UBE3C	XM_047421073.1	c.1810-3698A>G		intron_variant			XP_047277029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE3C	ENST00000348165.10	c.1810-3698A>G		intron_variant		1	NM_014671.3	ENSP00000309198	P1
UBE3C	ENST00000469336.1	n.277-3698A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62999 AN: 152066 Hom.: 16037 Cov.: 33

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.414 AC: 63065 AN: 152184 Hom.: 16056 Cov.: 33 AF XY: 0.412 AC XY: 30687 AN XY: 74400

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.400

Alfa AF: 0.303 Hom.: 15678

Bravo AF: 0.440

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.8
DANN	Benign	0.53

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: rs6979947; hg19: chr7-157005863;