10-51697364-G-A

Variant names:

• chr10-51697364-G-A
• rs11601
• NM_015235.3:c.*335C>T

Variant summary

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

The NM_015235.3(CSTF2T):​c.*335C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 222,910 control chromosomes in the GnomAD database, including 16,251 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 0.37 (13474 hom., cov: 32)
  • Exomes 𝑓: 0.26 (2777 hom.)
• Consequence: CSTF2T NM_015235.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 8 publications found

Genes affected

CSTF2T (HGNC:17086): (cleavage stimulation factor subunit 2 tau variant) Enables RNA binding activity. Predicted to be involved in pre-mRNA cleavage required for polyadenylation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PRKG1 (HGNC:9414): (protein kinase cGMP-dependent 1) Mammals have three different isoforms of cyclic GMP-dependent protein kinase (Ialpha, Ibeta, and II). These PRKG isoforms act as key mediators of the nitric oxide/cGMP signaling pathway and are important components of many signal transduction processes in diverse cell types. This PRKG1 gene on human chromosome 10 encodes the soluble Ialpha and Ibeta isoforms of PRKG by alternative transcript splicing. A separate gene on human chromosome 4, PRKG2, encodes the membrane-bound PRKG isoform II. The PRKG1 proteins play a central role in regulating cardiovascular and neuronal functions in addition to relaxing smooth muscle tone, preventing platelet aggregation, and modulating cell growth. This gene is most strongly expressed in all types of smooth muscle, platelets, cerebellar Purkinje cells, hippocampal neurons, and the lateral amygdala. Isoforms Ialpha and Ibeta have identical cGMP-binding and catalytic domains but differ in their leucine/isoleucine zipper and autoinhibitory sequences and therefore differ in their dimerization substrates and kinase enzyme activity. [provided by RefSeq, Sep 2011]

PRKG1 Gene-Disease associations (from GenCC):

• aortic aneurysm, familial thoracic 8

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• familial thoracic aortic aneurysm and aortic dissection

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet

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 (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015235.3. 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
	CSTF2T	NM_015235.3	MANE Select	c.*335C>T		3_prime_UTR	Exon 1 of 1	NP_056050.1
	PRKG1	NM_006258.4	MANE Select	c.593-107221G>A		intron	N/A	NP_006249.1
	PRKG1	NM_001098512.3		c.548-107221G>A		intron	N/A	NP_001091982.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSTF2T	ENST00000331173.6	TSL:6 MANE Select	c.*335C>T		3_prime_UTR	Exon 1 of 1	ENSP00000332444.4
	PRKG1	ENST00000373980.11	TSL:1 MANE Select	c.593-107221G>A		intron	N/A	ENSP00000363092.5
	PRKG1	ENST00000401604.8	TSL:5	c.548-107221G>A		intron	N/A	ENSP00000384200.4

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55894 AN: 151786 Hom.: 13422 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.326

GnomAD4 exome AF: 0.256 AC: 18187 AN: 71006 Hom.: 2777 Cov.: 0 AF XY: 0.257 AC XY: 9442 AN XY: 36736

African (AFR) AF: 0.700 AC: 1521 AN: 2174

American (AMR) AF: 0.325 AC: 1211 AN: 3724

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 535 AN: 2510

East Asian (EAS) AF: 0.389 AC: 1664 AN: 4278

South Asian (SAS) AF: 0.291 AC: 1217 AN: 4188

European-Finnish (FIN) AF: 0.233 AC: 682 AN: 2930

Middle Eastern (MID) AF: 0.242 AC: 86 AN: 356

European-Non Finnish (NFE) AF: 0.216 AC: 9968 AN: 46218

Other (OTH) AF: 0.282 AC: 1303 AN: 4628

GnomAD4 genome AF: 0.369 AC: 56015 AN: 151904 Hom.: 13474 Cov.: 32 AF XY: 0.366 AC XY: 27148 AN XY: 74218

African (AFR) AF: 0.693 AC: 28683 AN: 41416

American (AMR) AF: 0.319 AC: 4875 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.354 AC: 1825 AN: 5154

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2521 AN: 10502

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14943 AN: 67958

Other (OTH) AF: 0.327 AC: 691 AN: 2110

Alfa AF: 0.248 Hom.: 1872

Bravo AF: 0.392

Asia WGS AF: 0.344 AC: 1195 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.77
PhyloP100		0.0060
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: rs11601; hg19: chr10-53457124;