5-177007439-G-A

Position:

• chr5-177007439-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
UIMC1	XM_006714871.3	c.-9+15025C>T		intron_variant
UIMC1	XM_017009577.2	c.-9+15025C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UIMC1	ENST00000509236.5	c.-9+15025C>T		intron_variant		5
UIMC1	ENST00000515488.1	n.170+15025C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.546

Alfa AF: 0.520 Hom.: 12252

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs402511; hg19: chr5-176434440;