rs10803799

Variant names:

• chr2-165584037-A-C
• rs10803799
• NM_001172173.2:c.-23-11006A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CSRNP3	NM_001172173.2	c.-23-11006A>C		intron_variant	Intron 3 of 6	ENST00000651982.1	NP_001165644.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSRNP3	ENST00000651982.1	c.-23-11006A>C		intron_variant	Intron 3 of 6		NM_001172173.2	ENSP00000498841.1

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

African (AFR) AF: 0.211 AC: 8763 AN: 41488

American (AMR) AF: 0.427 AC: 6526 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1223 AN: 5166

South Asian (SAS) AF: 0.296 AC: 1428 AN: 4818

European-Finnish (FIN) AF: 0.317 AC: 3351 AN: 10568

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23094 AN: 67932

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.320 Hom.: 2969

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
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10803799; hg19: chr2-166440547;