chr2-165542124-A-G

Variant names:

• chr2-165542124-A-G
• rs1020626
• NM_001172173.2:c.-24+24163A>G

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+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
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001172173.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSRNP3	NM_001172173.2	MANE Select	c.-24+24163A>G		intron	N/A	NP_001165644.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSRNP3	ENST00000651982.1	MANE Select	c.-24+24163A>G		intron	N/A	ENSP00000498841.1
	CSRNP3	ENST00000314499.11	TSL:5	c.-24+24163A>G		intron	N/A	ENSP00000318258.7
	CSRNP3	ENST00000421875.5	TSL:5	c.-24+24163A>G		intron	N/A	ENSP00000412081.1

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

African (AFR) AF: 0.449 AC: 18570 AN: 41398

American (AMR) AF: 0.542 AC: 8262 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1847 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3816 AN: 5160

South Asian (SAS) AF: 0.510 AC: 2455 AN: 4818

European-Finnish (FIN) AF: 0.578 AC: 6113 AN: 10576

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40617 AN: 67938

Other (OTH) AF: 0.573 AC: 1207 AN: 2108

Alfa AF: 0.581 Hom.: 42435

Bravo AF: 0.548

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.49
PhyloP100		0.50
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: rs1020626; hg19: chr2-166398634;