rs6979947

Variant names:

• chr7-157213169-A-G
• rs6979947
• NM_014671.3:c.1810-3698A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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]

UBE3C Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with absent speech and movement and behavioral abnormalities

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014671.3. 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
	UBE3C	NM_014671.3	MANE Select	c.1810-3698A>G		intron	N/A	NP_055486.2	Q15386-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE3C	ENST00000348165.10	TSL:1 MANE Select	c.1810-3698A>G		intron	N/A	ENSP00000309198.8	Q15386-1
	UBE3C	ENST00000945962.1		c.1810-3698A>G		intron	N/A	ENSP00000616021.1
	UBE3C	ENST00000945960.1		c.1885-3698A>G		intron	N/A	ENSP00000616019.1

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

African (AFR) AF: 0.721 AC: 29915 AN: 41512

American (AMR) AF: 0.396 AC: 6051 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2179 AN: 5180

South Asian (SAS) AF: 0.300 AC: 1452 AN: 4832

European-Finnish (FIN) AF: 0.255 AC: 2703 AN: 10584

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18342 AN: 67996

Other (OTH) AF: 0.400 AC: 845 AN: 2114

Alfa AF: 0.319 Hom.: 38237

Bravo AF: 0.440

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.8
DANN	Benign	0.53
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6979947; hg19: chr7-157005863;