1-161269681-C-T

Variant names:

• chr1-161269681-C-T
• rs2501875
• NM_001102566.2:c.9+10698C>T

Variant summary

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

The NM_001102566.2(PCP4L1):​c.9+10698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,886 control chromosomes in the GnomAD database, including 15,637 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 0.45 (15637 hom., cov: 31)
• Consequence: PCP4L1 NM_001102566.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 5 publications found

Genes affected

PCP4L1 (HGNC:20448): (Purkinje cell protein 4 like 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102566.2. 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
	PCP4L1	NM_001102566.2	MANE Select	c.9+10698C>T		intron	N/A	NP_001096036.1	A6NKN8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCP4L1	ENST00000504449.2	TSL:1 MANE Select	c.9+10698C>T		intron	N/A	ENSP00000426296.1	A6NKN8
	PCP4L1	ENST00000874683.1		c.9+10698C>T		intron	N/A	ENSP00000544742.1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68088 AN: 151768 Hom.: 15608 Cov.: 31

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.449 AC: 68162 AN: 151886 Hom.: 15637 Cov.: 31 AF XY: 0.452 AC XY: 33521 AN XY: 74192

African (AFR) AF: 0.543 AC: 22482 AN: 41406

American (AMR) AF: 0.503 AC: 7681 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2174 AN: 5160

South Asian (SAS) AF: 0.378 AC: 1820 AN: 4810

European-Finnish (FIN) AF: 0.452 AC: 4759 AN: 10528

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26477 AN: 67930

Other (OTH) AF: 0.429 AC: 906 AN: 2110

Alfa AF: 0.406 Hom.: 48818

Bravo AF: 0.462

Asia WGS AF: 0.392 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.32
PhyloP100		0.19
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: rs2501875; hg19: chr1-161239471;