rs9285921

chr5-131240775-G-A

Variant summary

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

The XM_047417393.1(CDC42SE2):c.-705-14320G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,144 control chromosomes in the GnomAD database, including 3,036 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 0.13 (3036 hom., cov: 32)
• Consequence: CDC42SE2 XM_047417393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

CDC42SE2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDC42SE2	XM_047417393.1	c.-705-14320G>A		intron_variant
CDC42SE2	XM_047417396.1	c.-784+7701G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19729 AN: 152026 Hom.: 3028 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0657

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.00878

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.130 AC: 19770 AN: 152144 Hom.: 3036 Cov.: 32 AF XY: 0.124 AC XY: 9234 AN XY: 74386

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.0656

Gnomad4 ASJ AF: 0.0721

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0446

Gnomad4 FIN AF: 0.00878

Gnomad4 NFE AF: 0.0372

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0751 Hom.: 259

Bravo AF: 0.145

Asia WGS AF: 0.0450 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.30
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285921; hg19: chr5-130576468;