13-113239922-G-T

Variant names:

• chr13-113239922-G-T
• rs1885688
• NM_001008895.4:c.1035+371G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CUL4A	NM_001008895.4	c.1035+371G>T		intron_variant	Intron 10 of 19	ENST00000375440.9	NP_001008895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUL4A	ENST00000375440.9	c.1035+371G>T		intron_variant	Intron 10 of 19	1	NM_001008895.4	ENSP00000364589.4

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

African (AFR) AF: 0.139 AC: 5786 AN: 41480

American (AMR) AF: 0.342 AC: 5228 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2877 AN: 5186

South Asian (SAS) AF: 0.432 AC: 2077 AN: 4810

European-Finnish (FIN) AF: 0.287 AC: 3022 AN: 10538

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16005 AN: 67986

Other (OTH) AF: 0.238 AC: 502 AN: 2112

Alfa AF: 0.232 Hom.: 5066

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
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1885688; hg19: chr13-113894236; COSMIC: COSV107363040; COSMIC: COSV107363040;