rs10930170

Variant names:

• chr2-165542957-G-A
• rs10930170
• NM_001172173.2:c.-24+24996G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.88).
• 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 rank	MANE	Protein	UniProt
CSRNP3	NM_001172173.2	c.-24+24996G>A		intron_variant	Intron 3 of 6	ENST00000651982.1	NP_001165644.1
CSRNP3	XM_024453155.2	c.-24+24996G>A		intron_variant	Intron 4 of 7		XP_024308923.1
CSRNP3	XM_047445908.1	c.-24+24996G>A		intron_variant	Intron 3 of 6		XP_047301864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSRNP3	ENST00000651982.1	c.-24+24996G>A		intron_variant	Intron 3 of 6		NM_001172173.2	ENSP00000498841.1

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

African (AFR) AF: 0.593 AC: 24564 AN: 41428

American (AMR) AF: 0.648 AC: 9894 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2187 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4017 AN: 5166

South Asian (SAS) AF: 0.582 AC: 2806 AN: 4824

European-Finnish (FIN) AF: 0.644 AC: 6809 AN: 10570

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47178 AN: 67960

Other (OTH) AF: 0.681 AC: 1439 AN: 2112

Alfa AF: 0.679 Hom.: 107947

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
PhyloP100		-0.20
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: rs10930170; hg19: chr2-166399467;