2-165514316-A-C

Variant names:

• chr2-165514316-A-C
• rs6432832
• NM_001172173.2:c.-112-3557A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001172173.2(CSRNP3):​c.-112-3557A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,202 control chromosomes in the GnomAD database, including 41,454 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 0.73 (41454 hom., cov: 34)
• Consequence: CSRNP3 NM_001172173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSRNP3	NM_001172173.2	c.-112-3557A>C		intron_variant	Intron 2 of 6	ENST00000651982.1	NP_001165644.1
CSRNP3	XM_024453155.2	c.-112-3557A>C		intron_variant	Intron 3 of 7		XP_024308923.1
CSRNP3	XM_047445908.1	c.-112-3557A>C		intron_variant	Intron 2 of 6		XP_047301864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSRNP3	ENST00000651982.1	c.-112-3557A>C		intron_variant	Intron 2 of 6		NM_001172173.2	ENSP00000498841.1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111175 AN: 152084 Hom.: 41387 Cov.: 34

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.731 AC: 111301 AN: 152202 Hom.: 41454 Cov.: 34 AF XY: 0.731 AC XY: 54367 AN XY: 74398

African (AFR) AF: 0.870 AC: 36121 AN: 41532

American (AMR) AF: 0.732 AC: 11195 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2229 AN: 3466

East Asian (EAS) AF: 0.796 AC: 4111 AN: 5164

South Asian (SAS) AF: 0.616 AC: 2972 AN: 4824

European-Finnish (FIN) AF: 0.698 AC: 7393 AN: 10594

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45060 AN: 68008

Other (OTH) AF: 0.707 AC: 1497 AN: 2116

Alfa AF: 0.700 Hom.: 19988

Bravo AF: 0.742

Asia WGS AF: 0.726 AC: 2521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.66
PhyloP100		-1.4
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: rs6432832; hg19: chr2-166370826;