Variant rs7187167 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.770

Variant links:

Genes affected

LOC124903624 (HGNC:):

LOC124903624 links:

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]

UBE2I links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
LOC124903624	XR_007064939.1 linkuse as main transcript	n.398A>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.691

AC:

104917

AN:

151826

Hom.:

36697

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.725

AC XY:

AN XY:

show subpopulations

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.:

AF XY:

0.695

AC XY:

51634

AN XY:

74266

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over