rs1020626

Positions:

• chr2-165542124-A-G

Variant summary

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

The NM_001172173.2(CSRNP3):​c.-24+24163A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,908 control chromosomes in the GnomAD database, including 23,582 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 0.55 (23582 hom., cov: 32)
• Consequence: CSRNP3 NM_001172173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSRNP3	NM_001172173.2	c.-24+24163A>G		intron_variant		ENST00000651982.1
CSRNP3	XM_024453155.2	c.-24+24163A>G		intron_variant
CSRNP3	XM_047445908.1	c.-24+24163A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSRNP3	ENST00000651982.1	c.-24+24163A>G		intron_variant			NM_001172173.2	P1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83537 AN: 151792 Hom.: 23578 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.550 AC: 83570 AN: 151908 Hom.: 23582 Cov.: 32 AF XY: 0.550 AC XY: 40858 AN XY: 74260

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.573

Alfa AF: 0.586 Hom.: 33825

Bravo AF: 0.548

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.49

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: rs1020626; hg19: chr2-166398634;