rs10803799

chr2-165584037-A-C

Variant summary

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

The NM_001172173.2(CSRNP3):c.-23-11006A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,034 control chromosomes in the GnomAD database, including 7,490 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 0.31 (7490 hom., cov: 32)
• Consequence: CSRNP3 NM_001172173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831

Genes affected

CSRNP3 (HGNC:30729): (cysteine and serine rich nuclear protein 3) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Predicted to be involved in positive regulation of apoptotic process and positive regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSRNP3	NM_001172173.2	c.-23-11006A>C		intron_variant		ENST00000651982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSRNP3	ENST00000651982.1	c.-23-11006A>C		intron_variant			NM_001172173.2	P1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46436 AN: 151916 Hom.: 7482 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.306 AC: 46463 AN: 152034 Hom.: 7490 Cov.: 32 AF XY: 0.305 AC XY: 22661 AN XY: 74308

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.324

Alfa AF: 0.328 Hom.: 1671

Bravo AF: 0.311

Asia WGS AF: 0.285 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10803799; hg19: chr2-166440547;