rs2473277

Variant names:

• chr1-22035352-G-A
• rs2473277
• ENST00000695856.1:c.-51+9713G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-22035352-G-A
• chr1-22035352-G-C
• chr1-22035352-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000695856.1(ENSG00000289694):​c.-51+9713G>A variant causes a intron 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: ENSG00000289694 ENST00000695856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 29 publications found

Genes affected

ENSG00000289694 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289694	ENST00000695856.1	c.-51+9713G>A		intron_variant	Intron 1 of 5			ENSP00000512221.1
ENSG00000289694	ENST00000695855.1	c.-51+9980G>A		intron_variant	Intron 1 of 5			ENSP00000512220.1
CDC42-AS1	ENST00000649486.1	n.142-3485C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.760 AC: 31109 AN: 40958

American (AMR) AF: 0.441 AC: 6587 AN: 14942

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2053 AN: 3464

East Asian (EAS) AF: 0.367 AC: 1884 AN: 5128

South Asian (SAS) AF: 0.601 AC: 2871 AN: 4776

European-Finnish (FIN) AF: 0.453 AC: 4510 AN: 9964

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35940 AN: 67830

Other (OTH) AF: 0.601 AC: 1258 AN: 2094

Alfa AF: 0.540 Hom.: 75937

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2473277; hg19: chr1-22361845;