rs7187167

chr16-1299208-T-Cchr16-1299208-T-G

Variant summary

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

The XR_007064939.1(LOC124903624):n.398A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,016 control chromosomes in the GnomAD database, including 36,730 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 0.69 (36709 hom., cov: 32)
  • Exomes 𝑓: 0.76 (21 hom.)
• Consequence: LOC124903624 XR_007064939.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770

Genes affected

LOC124903624 (HGNC:):

UBE2I (HGNC:12485): (ubiquitin conjugating enzyme E2 I) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Four alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903624	XR_007064939.1	n.398A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000711365.1	n.124+1381A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104917 AN: 151826 Hom.: 36697 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.672

GnomAD4 exome AF: 0.764 AC: 55 AN: 72 Hom.: 21 Cov.: 0 AF XY: 0.725 AC XY: 29 AN XY: 40

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.696

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.691 AC: 104976 AN: 151944 Hom.: 36709 Cov.: 32 AF XY: 0.695 AC XY: 51634 AN XY: 74266

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.674

Alfa AF: 0.716 Hom.: 74524

Bravo AF: 0.675

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.5
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7187167; hg19: chr16-1349209;