chr2-165565500-G-A

Variant names:

• chr2-165565500-G-A
• rs16850914
• NM_001172173.2:c.-23-29543G>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.-23-29543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,960 control chromosomes in the GnomAD database, including 3,378 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 0.20 (3378 hom., cov: 32)
• Consequence: CSRNP3 NM_001172173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.688
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 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.-23-29543G>A		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.-23-29543G>A		intron	N/A	ENSP00000498841.1
	CSRNP3	ENST00000314499.11	TSL:5	c.-23-29543G>A		intron	N/A	ENSP00000318258.7
	CSRNP3	ENST00000421875.5	TSL:5	c.-23-29543G>A		intron	N/A	ENSP00000412081.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31082 AN: 151842 Hom.: 3379 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.205 AC: 31098 AN: 151960 Hom.: 3378 Cov.: 32 AF XY: 0.208 AC XY: 15453 AN XY: 74292

African (AFR) AF: 0.145 AC: 6020 AN: 41482

American (AMR) AF: 0.265 AC: 4036 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1309 AN: 5170

South Asian (SAS) AF: 0.283 AC: 1359 AN: 4810

European-Finnish (FIN) AF: 0.254 AC: 2692 AN: 10588

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14155 AN: 67898

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.208 Hom.: 4657

Bravo AF: 0.202

Asia WGS AF: 0.266 AC: 924 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		0.69
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: rs16850914; hg19: chr2-166422010;