2-165572871-T-G

Variant names:

• chr2-165572871-T-G
• rs10497264
• NM_001172173.2:c.-23-22172T>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.-23-22172T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,042 control chromosomes in the GnomAD database, including 10,183 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 0.36 (10183 hom., cov: 32)
• Consequence: CSRNP3 NM_001172173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSRNP3	NM_001172173.2	c.-23-22172T>G		intron_variant	Intron 3 of 6	ENST00000651982.1	NP_001165644.1
CSRNP3	NM_024969.3	c.-24+284T>G		intron_variant	Intron 1 of 4		NP_079245.2
CSRNP3	XM_024453155.2	c.-23-22172T>G		intron_variant	Intron 4 of 7		XP_024308923.1
CSRNP3	XM_047445908.1	c.-23-22172T>G		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.-23-22172T>G		intron_variant	Intron 3 of 6		NM_001172173.2	ENSP00000498841.1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55196 AN: 151924 Hom.: 10183 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.363 AC: 55219 AN: 152042 Hom.: 10183 Cov.: 32 AF XY: 0.367 AC XY: 27269 AN XY: 74332

African (AFR) AF: 0.317 AC: 13152 AN: 41486

American (AMR) AF: 0.274 AC: 4191 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2351 AN: 5164

South Asian (SAS) AF: 0.482 AC: 2323 AN: 4824

European-Finnish (FIN) AF: 0.408 AC: 4302 AN: 10554

Middle Eastern (MID) AF: 0.376 AC: 109 AN: 290

European-Non Finnish (NFE) AF: 0.387 AC: 26289 AN: 67960

Other (OTH) AF: 0.341 AC: 720 AN: 2110

Alfa AF: 0.387 Hom.: 3720

Bravo AF: 0.349

Asia WGS AF: 0.425 AC: 1467 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.73
PhyloP100		-0.18
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: rs10497264; hg19: chr2-166429381;