rs924693

Variant names:

• chr11-19222830-C-T
• rs924693
• ENST00000527978.2:n.146-2004C>T

Variant summary

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

The ENST00000527978.2(CSRP3-AS1):​n.146-2004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,906 control chromosomes in the GnomAD database, including 8,743 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 0.33 (8743 hom., cov: 32)
• Consequence: CSRP3-AS1 ENST00000527978.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 7 publications found

Genes affected

CSRP3-AS1 (HGNC:54183): (CSRP3 and E2F8 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527978.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSRP3-AS1	NR_183675.1		n.207+25911C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSRP3-AS1	ENST00000527978.2	TSL:5	n.146-2004C>T		intron	N/A
	CSRP3-AS1	ENST00000789312.1		n.107-2004C>T		intron	N/A
	CSRP3-AS1	ENST00000789313.1		n.103+12905C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50642 AN: 151788 Hom.: 8736 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.334 AC: 50669 AN: 151906 Hom.: 8743 Cov.: 32 AF XY: 0.343 AC XY: 25435 AN XY: 74224

African (AFR) AF: 0.277 AC: 11477 AN: 41432

American (AMR) AF: 0.405 AC: 6191 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2456 AN: 5166

South Asian (SAS) AF: 0.382 AC: 1834 AN: 4804

European-Finnish (FIN) AF: 0.443 AC: 4657 AN: 10518

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.322 AC: 21895 AN: 67938

Other (OTH) AF: 0.348 AC: 731 AN: 2100

Alfa AF: 0.331 Hom.: 14589

Bravo AF: 0.331

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs924693; hg19: chr11-19244377;