6-47973528-A-G

Position:

• chr6-47973528-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001384253.1(PTCHD4):​c.898+35106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 152,316 control chromosomes in the GnomAD database, including 71,696 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 0.97 (71696 hom., cov: 32)
• Consequence: PTCHD4 NM_001384253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD4	NM_001384253.1	c.898+35106T>C		intron_variant		ENST00000339488.9	NP_001371182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCHD4	ENST00000339488.9	c.898+35106T>C		intron_variant		2	NM_001384253.1	ENSP00000341914.5
PTCHD4	ENST00000398738.3	c.898+35106T>C		intron_variant		1		ENSP00000381722.3
PTCHD4	ENST00000679966.1	c.1072+35106T>C		intron_variant				ENSP00000506133.1

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147667 AN: 152200 Hom.: 71643 Cov.: 32

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.970 AC: 147778 AN: 152316 Hom.: 71696 Cov.: 32 AF XY: 0.970 AC XY: 72213 AN XY: 74482

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.996

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.964

Alfa AF: 0.970 Hom.: 8974

Bravo AF: 0.969

Asia WGS AF: 0.994 AC: 3456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.072
DANN	Benign	0.33

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: rs2814478; hg19: chr6-47941264;