rs2473277

chr1-22035352-G-A

Variant summary

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

The ENST00000649486.1(CDC42-AS1):n.142-3485C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 150,360 control chromosomes in the GnomAD database, including 26,095 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 (26095 hom., cov: 28)
• Consequence: CDC42-AS1 ENST00000649486.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

CDC42-AS1 (HGNC:54314): (CDC42 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC42-AS1	ENST00000649486.1	n.142-3485C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.575 AC: 86455 AN: 150260 Hom.: 26052 Cov.: 28

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.576 AC: 86548 AN: 150360 Hom.: 26095 Cov.: 28 AF XY: 0.568 AC XY: 41595 AN XY: 73176

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.601

Alfa AF: 0.530 Hom.: 44852

Bravo AF: 0.579

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.81
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2473277; hg19: chr1-22361845;