rs11271054

Variant names:

• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCT
• rs11271054
• NM_014801.4:c.4606-11_4606-10insAGAATAGCTGTGAGGACTCAAAATCTTGCTTT

Your query was ambiguous. Multiple possible variants found:

• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCT
• chr1-233017164-A-AAAAGCAAGATTTGGAGTCCTCACAGCTATTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAATCCTCACAGCTATTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTACTCACAGCTATTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAACTATTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCAATTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTAGTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATACT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCG
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTCTTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTGTTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTTTTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACATCTATTCT
• chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCATAGCTATTCT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_014801.4(PCNX2):​c.4606-11_4606-10insAGAATAGCTGTGAGGACTCAAAATCTTGCTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,392,556 control chromosomes in the GnomAD database, including 90,592 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.43 (14805 hom., cov: 22)
  • Exomes 𝑓: 0.35 (90592 hom.)
  • Failed GnomAD Quality Control
• Consequence: PCNX2 NM_014801.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.581
• Publications: 1 publications found

Genes affected

PCNX2 (HGNC:8736): (pecanex 2) This gene contains coding mononucleotide repeats that are associated with tumors of high mcrosatellite instability (MSI-H). Defects in this gene are involved in the tumorigenesis of MSI-H colorectal carcinomas. [provided by RefSeq, Jun 2016]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCT is Benign according to our data. Variant chr1-233017164-A-AAAAGCAAGATTTTGAGTCCTCACAGCTATTCT is described in ClinVar as Benign. ClinVar VariationId is 2975927.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014801.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCNX2	NM_014801.4	MANE Select	c.4606-11_4606-10insAGAATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	NP_055616.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCNX2	ENST00000258229.14	TSL:5 MANE Select	c.4606-11_4606-10insAGAATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	ENSP00000258229.8	A6NKB5-1
	PCNX2	ENST00000912675.1		c.4231-11_4231-10insAGAATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	ENSP00000582734.1
	PCNX2	ENST00000344698.6	TSL:2	c.562-11_562-10insAGAATAGCTGTGAGGACTCAAAATCTTGCTTT		intron	N/A	ENSP00000340759.2	A6NKB5-3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64670 AN: 151338 Hom.: 14782 Cov.: 22

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.439

GnomAD4 exome AF: 0.352 AC: 489728 AN: 1392556 Hom.: 90592 Cov.: 32 AF XY: 0.349 AC XY: 239735 AN XY: 687096

African (AFR) AF: 0.605 AC: 19095 AN: 31586

American (AMR) AF: 0.457 AC: 19816 AN: 43344

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 9320 AN: 25410

East Asian (EAS) AF: 0.514 AC: 19793 AN: 38496

South Asian (SAS) AF: 0.299 AC: 24875 AN: 83316

European-Finnish (FIN) AF: 0.314 AC: 16601 AN: 52882

Middle Eastern (MID) AF: 0.410 AC: 2099 AN: 5120

European-Non Finnish (NFE) AF: 0.338 AC: 356849 AN: 1054934

Other (OTH) AF: 0.370 AC: 21280 AN: 57468

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.427 AC: 64746 AN: 151458 Hom.: 14805 Cov.: 22 AF XY: 0.426 AC XY: 31480 AN XY: 73978

African (AFR) AF: 0.592 AC: 24384 AN: 41194

American (AMR) AF: 0.434 AC: 6607 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2841 AN: 5136

South Asian (SAS) AF: 0.311 AC: 1491 AN: 4798

European-Finnish (FIN) AF: 0.306 AC: 3213 AN: 10514

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.349 AC: 23701 AN: 67838

Other (OTH) AF: 0.440 AC: 925 AN: 2100

Alfa AF: 0.317 Hom.: 1305

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11271054; hg19: chr1-233152910; COSMIC: COSV50790663;