rs601923

Positions:

• chr5-176990385-C-G

Variant summary

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

The NM_001199298.2(UIMC1):​c.-8-7762G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,714 control chromosomes in the GnomAD database, including 26,993 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 (26993 hom., cov: 29)
• Consequence: UIMC1 NM_001199298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UIMC1	NM_001199298.2	c.-8-7762G>C		intron_variant		ENST00000511320.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UIMC1	ENST00000511320.6	c.-8-7762G>C		intron_variant		1	NM_001199298.2	P1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87435 AN: 151596 Hom.: 26940 Cov.: 29

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.577 AC: 87544 AN: 151714 Hom.: 26993 Cov.: 29 AF XY: 0.573 AC XY: 42477 AN XY: 74122

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.546

Alfa AF: 0.548 Hom.: 3332

Bravo AF: 0.580

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs601923; hg19: chr5-176417386;