chr5-177007439-G-A

Variant names:

• chr5-177007439-G-A
• rs402511
• ENST00000509236.5:c.-9+15025C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509236.5(UIMC1):​c.-9+15025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,876 control chromosomes in the GnomAD database, including 27,065 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 0.58 (27065 hom., cov: 31)
• Consequence: UIMC1 ENST00000509236.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 20 publications found

Genes affected

UIMC1 (HGNC:30298): (ubiquitin interaction motif containing 1) This gene encodes a nuclear protein that interacts with Brca1 (breast cancer 1) in a complex to recognize and repair DNA lesions. This protein binds ubiquitinated lysine 63 of histone H2A and H2AX. This protein may also function as a repressor of transcription. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

UIMC1 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UIMC1	XM_006714871.3	c.-9+15025C>T		intron_variant	Intron 1 of 14		XP_006714934.1
UIMC1	XM_017009577.2	c.-9+15025C>T		intron_variant	Intron 1 of 12		XP_016865066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UIMC1	ENST00000509236.5	c.-9+15025C>T		intron_variant	Intron 1 of 5	5		ENSP00000423885.1
UIMC1	ENST00000515488.1	n.170+15025C>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87630 AN: 151758 Hom.: 27012 Cov.: 31

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.578 AC: 87739 AN: 151876 Hom.: 27065 Cov.: 31 AF XY: 0.574 AC XY: 42600 AN XY: 74218

African (AFR) AF: 0.811 AC: 33620 AN: 41448

American (AMR) AF: 0.424 AC: 6481 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2531 AN: 5156

South Asian (SAS) AF: 0.501 AC: 2415 AN: 4820

European-Finnish (FIN) AF: 0.499 AC: 5241 AN: 10494

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33763 AN: 67908

Other (OTH) AF: 0.546 AC: 1152 AN: 2108

Alfa AF: 0.540 Hom.: 21533

Bravo AF: 0.580

Asia WGS AF: 0.544 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.67
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs402511; hg19: chr5-176434440;