rs1885688

chr13-113239922-G-T

Variant summary

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

The NM_001008895.4(CUL4A):c.1035+371G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,068 control chromosomes in the GnomAD database, including 5,136 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 0.24 (5136 hom., cov: 33)
• Consequence: CUL4A NM_001008895.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

Genes affected

CUL4A (HGNC:2554): (cullin 4A) CUL4A is the ubiquitin ligase component of a multimeric complex involved in the degradation of DNA damage-response proteins (Liu et al., 2009 [PubMed 19481525]).[supplied by OMIM, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUL4A	NM_001008895.4	c.1035+371G>T		intron_variant		ENST00000375440.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUL4A	ENST00000375440.9	c.1035+371G>T		intron_variant		1	NM_001008895.4	P1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36342 AN: 151950 Hom.: 5125 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.239 AC: 36387 AN: 152068 Hom.: 5136 Cov.: 33 AF XY: 0.249 AC XY: 18488 AN XY: 74322

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.238

Alfa AF: 0.232 Hom.: 3797

Bravo AF: 0.235

Asia WGS AF: 0.507 AC: 1757 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	0.20
Dann	Benign	0.30

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: rs1885688; hg19: chr13-113894236;