rs10930170

Positions:

• chr2-165542957-G-A

Variant summary

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

The NM_001172173.2(CSRNP3):​c.-24+24996G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,000 control chromosomes in the GnomAD database, including 32,962 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 0.66 (32962 hom., cov: 32)
• Consequence: CSRNP3 NM_001172173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSRNP3	NM_001172173.2	c.-24+24996G>A		intron_variant		ENST00000651982.1
CSRNP3	XM_024453155.2	c.-24+24996G>A		intron_variant
CSRNP3	XM_047445908.1	c.-24+24996G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSRNP3	ENST00000651982.1	c.-24+24996G>A		intron_variant			NM_001172173.2	P1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99619 AN: 151882 Hom.: 32958 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.656 AC: 99656 AN: 152000 Hom.: 32962 Cov.: 32 AF XY: 0.653 AC XY: 48525 AN XY: 74288

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.681

Alfa AF: 0.684 Hom.: 48704

Bravo AF: 0.658

Asia WGS AF: 0.662 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.67

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: rs10930170; hg19: chr2-166399467;