1-22047131-C-T

Variant names:

• chr1-22047131-C-T
• rs2501276
• ENST00000695856.1:c.-51+21492C>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+21492C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 149,808 control chromosomes in the GnomAD database, including 563 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 0.081 (563 hom., cov: 30)
• Consequence: ENSG00000289694 ENST00000695856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 12 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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+21492C>T		intron_variant	Intron 1 of 5			ENSP00000512221.1
ENSG00000289694	ENST00000695855.1	c.-51+21759C>T		intron_variant	Intron 1 of 5			ENSP00000512220.1
CDC42-AS1	ENST00000649486.1	n.141+5656G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12130 AN: 149752 Hom.: 558 Cov.: 30

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.0609

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0972

Gnomad MID AF: 0.0526

Gnomad NFE AF: 0.0968

Gnomad OTH AF: 0.0853

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

GnomAD4 genome AF: 0.0811 AC: 12149 AN: 149808 Hom.: 563 Cov.: 30 AF XY: 0.0810 AC XY: 5911 AN XY: 72932

African (AFR) AF: 0.0614 AC: 2494 AN: 40638

American (AMR) AF: 0.0632 AC: 946 AN: 14962

Ashkenazi Jewish (ASJ) AF: 0.0609 AC: 210 AN: 3450

East Asian (EAS) AF: 0.0170 AC: 87 AN: 5114

South Asian (SAS) AF: 0.143 AC: 677 AN: 4730

European-Finnish (FIN) AF: 0.0972 AC: 961 AN: 9888

Middle Eastern (MID) AF: 0.0603 AC: 17 AN: 282

European-Non Finnish (NFE) AF: 0.0968 AC: 6558 AN: 67768

Other (OTH) AF: 0.0908 AC: 188 AN: 2070

Alfa AF: 0.0870 Hom.: 2742

Bravo AF: 0.0738

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.57
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2501276; hg19: chr1-22373624;