1-44830004-A-G

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_003738.5(PTCH2):c.840T>C(p.Ser280=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00629 in 1,614,010 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0064 ( 52 hom. )

Consequence

PTCH2
NM_003738.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -3.32

Variant links:

Genes affected

PTCH2 (HGNC:9586): (patched 2) This gene encodes a transmembrane receptor of the patched gene family. The encoded protein may function as a tumor suppressor in the hedgehog signaling pathway. Alterations in this gene have been associated with nevoid basal cell carcinoma syndrome, basal cell carcinoma, medulloblastoma, and susceptibility to congenital macrostomia. Alternatively spliced transcript variants have been described.[provided by RefSeq, Oct 2009]

PTCH2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 1-44830004-A-G is Benign according to our data. Variant chr1-44830004-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 239562.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-44830004-A-G is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-3.32 with no splicing effect.

BS2

High AC in GnomAd at 788 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCH2	NM_003738.5 linkuse as main transcript	c.840T>C	p.Ser280=	synonymous_variant	7/22	ENST00000372192.4
PTCH2	NM_001166292.2 linkuse as main transcript	c.840T>C	p.Ser280=	synonymous_variant	7/23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCH2	ENST00000372192.4 linkuse as main transcript	c.840T>C	p.Ser280=	synonymous_variant	7/22	1	NM_003738.5	P2	Q9Y6C5-1
PTCH2	ENST00000447098.6 linkuse as main transcript	c.840T>C	p.Ser280=	synonymous_variant	7/23	1		A2	Q9Y6C5-2

Frequencies

GnomAD3 genomes

AF:

0.00518

AC:

788

AN:

152082

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000942

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00255

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00676

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.0172

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00707

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00535

AC:

1343

AN:

251018

Hom.:

AF XY:

0.00509

AC XY:

691

AN XY:

135746

show subpopulations

Gnomad AFR exome

AF:

0.000866

Gnomad AMR exome

AF:

0.00179

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00250

Gnomad SAS exome

AF:

0.000327

Gnomad FIN exome

AF:

0.0182

Gnomad NFE exome

AF:

0.00693

Gnomad OTH exome

AF:

0.00506

GnomAD4 exome

AF:

0.00640

AC:

9362

AN:

1461810

Hom.:

Cov.:

AF XY:

0.00632

AC XY:

4595

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.000538

Gnomad4 AMR exome

AF:

0.00235

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0133

Gnomad4 SAS exome

AF:

0.000487

Gnomad4 FIN exome

AF:

0.0184

Gnomad4 NFE exome

AF:

0.00666

Gnomad4 OTH exome

AF:

0.00457

GnomAD4 genome

AF:

0.00518

AC:

788

AN:

152200

Hom.:

Cov.:

AF XY:

0.00547

AC XY:

407

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.000939

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00677

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.0172

Gnomad4 NFE

AF:

0.00707

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00576

Hom.:

Bravo

AF:

0.00372

Asia WGS

AF:

0.00606

AC:

AN:

3478

EpiCase

AF:

0.00425

EpiControl

AF:

0.00439

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	PTCH2: BP4, BP7, BS2 -

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Genome Diagnostics Laboratory, Amsterdam University Medical Center

- -

Basal cell carcinoma, susceptibility to, 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Jul 07, 2023

- -

Gorlin syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

Cadd

Benign

0.080

Dann

Benign

0.22

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over