12-42368912-T-G

Variant names:

• chr12-42368912-T-G
• rs752767
• NM_201439.2:c.300-5951T>G

Variant summary

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

The NM_201439.2(PPHLN1):​c.300-5951T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,174 control chromosomes in the GnomAD database, including 7,333 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 0.28 (7333 hom., cov: 32)
• Consequence: PPHLN1 NM_201439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 3 publications found

Genes affected

PPHLN1 (HGNC:19369): (periphilin 1) The protein encoded by this gene is one of the several proteins that become sequentially incorporated into the cornified cell envelope during the terminal differentiation of keratinocyte at the outer layers of epidermis. This protein interacts with periplakin, which is known as a precursor of the cornified cell envelope. The cellular localization pattern and insolubility of this protein suggest that it may play a role in epithelial differentiation and contribute to epidermal integrity and barrier formation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201439.2. 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
	PPHLN1	NM_201439.2	MANE Select	c.300-5951T>G		intron	N/A	NP_958847.1
	PPHLN1	NM_001364827.2		c.300-5951T>G		intron	N/A	NP_001351756.1
	PPHLN1	NM_016488.7		c.300-5951T>G		intron	N/A	NP_057572.5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPHLN1	ENST00000358314.12	TSL:2 MANE Select	c.300-5951T>G		intron	N/A	ENSP00000351066.7
	PPHLN1	ENST00000395568.6	TSL:1	c.300-5951T>G		intron	N/A	ENSP00000378935.2
	PPHLN1	ENST00000432191.6	TSL:1	c.135-5951T>G		intron	N/A	ENSP00000393965.2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42640 AN: 152056 Hom.: 7334 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.280 AC: 42644 AN: 152174 Hom.: 7333 Cov.: 32 AF XY: 0.278 AC XY: 20699 AN XY: 74374

African (AFR) AF: 0.0847 AC: 3517 AN: 41544

American (AMR) AF: 0.321 AC: 4906 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1288 AN: 3466

East Asian (EAS) AF: 0.178 AC: 925 AN: 5184

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4826

European-Finnish (FIN) AF: 0.384 AC: 4060 AN: 10574

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25802 AN: 67972

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.210 Hom.: 600

Bravo AF: 0.271

Asia WGS AF: 0.204 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.9
DANN	Benign	0.85
PhyloP100		1.3
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: rs752767; hg19: chr12-42762714;