NM_001384253.1:c.*4086C>A

Variant names:

• chr6-47874217-G-T
• rs4715047
• NM_001384253.1:c.*4086C>A

Variant summary

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

The NM_001384253.1(PTCHD4):​c.*4086C>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 0.515 in 151,426 control chromosomes in the GnomAD database, including 20,708 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 0.52 (20708 hom., cov: 31)
• Consequence: PTCHD4 NM_001384253.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 1 publications found

Genes affected

PTCHD4 (HGNC:21345): (patched domain containing 4) Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000304494 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD4	NM_001384253.1	c.*4086C>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000339488.9	NP_001371182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD4	ENST00000339488.9	c.*4086C>A		3_prime_UTR_variant	Exon 5 of 5	2	NM_001384253.1	ENSP00000341914.5
ENSG00000304494	ENST00000803765.1	n.662G>T		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.515 AC: 77987 AN: 151308 Hom.: 20687 Cov.: 31

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.515 AC: 78053 AN: 151426 Hom.: 20708 Cov.: 31 AF XY: 0.519 AC XY: 38423 AN XY: 73964

African (AFR) AF: 0.405 AC: 16776 AN: 41378

American (AMR) AF: 0.654 AC: 9927 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1970 AN: 3460

East Asian (EAS) AF: 0.748 AC: 3826 AN: 5114

South Asian (SAS) AF: 0.549 AC: 2639 AN: 4804

European-Finnish (FIN) AF: 0.521 AC: 5486 AN: 10532

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35663 AN: 67652

Other (OTH) AF: 0.549 AC: 1157 AN: 2108

Alfa AF: 0.523 Hom.: 10831

Bravo AF: 0.522

Asia WGS AF: 0.632 AC: 2196 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.50
DANN	Benign	0.53
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4715047; hg19: chr6-47841953;