12-27963178-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000395868.7(PTHLH):c.*166G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0448 in 1,499,164 control chromosomes in the GnomAD database, including 2,125 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.045 (228 hom., cov: 32)
  • Exomes 𝑓: 0.045 (1897 hom.)
• Consequence: PTHLH ENST00000395868.7 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.96

Genes affected

PTHLH (HGNC:9607): (parathyroid hormone like hormone) The protein encoded by this gene is a member of the parathyroid hormone family. This hormone, via its receptor, PTHR1, regulates endochondral bone development and epithelial-mesenchymal interactions during the formation of the mammary glands and teeth. It is responsible for most cases of humoral hypercalcemia of malignancy, and mutations in this gene are associated with brachydactyly type E2 (BDE2). Alternatively spliced transcript variants have been found for this gene. There is also evidence for alternative translation initiation from non-AUG (CUG and GUG) start sites, downstream of the initiator AUG codon, resulting in nuclear forms of this hormone. [provided by RefSeq, Nov 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 12-27963178-C-T is Benign according to our data. Variant chr12-27963178-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1193892.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTHLH	NM_198965.2	c.524+170G>A		intron_variant		ENST00000545234.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTHLH	ENST00000545234.6	c.524+170G>A		intron_variant		5	NM_198965.2	A1
	ENST00000538113.1	n.90+4572C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6810 AN: 152090 Hom.: 226 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0435

GnomAD4 exome AF: 0.0447 AC: 60274 AN: 1346956 Hom.: 1897 Cov.: 32 AF XY: 0.0456 AC XY: 30061 AN XY: 659728

Gnomad4 AFR exome AF: 0.0242

Gnomad4 AMR exome AF: 0.157

Gnomad4 ASJ exome AF: 0.0734

Gnomad4 EAS exome AF: 0.115

Gnomad4 SAS exome AF: 0.0887

Gnomad4 FIN exome AF: 0.0220

Gnomad4 NFE exome AF: 0.0363

Gnomad4 OTH exome AF: 0.0519

GnomAD4 genome AF: 0.0449 AC: 6828 AN: 152208 Hom.: 228 Cov.: 32 AF XY: 0.0446 AC XY: 3321 AN XY: 74396

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0906

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0351

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0384 Hom.: 170

Bravo AF: 0.0519

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 16, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.8
Dann	Benign	0.80

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

Other links and lift over

dbSNP: rs2796; hg19: chr12-28116111;