rs7538876

Positions:

• chr1-17395867-G-A

Variant summary

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

The NM_207421.4(PADI6):​c.1618+204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,052 control chromosomes in the GnomAD database, including 10,202 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.36 (10202 hom., cov: 33)
• Consequence: PADI6 NM_207421.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.501

Genes affected

PADI6 (HGNC:20449): (peptidyl arginine deiminase 6) This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. This protein may play a role in cytoskeletal reorganization in the egg and in early embryo development. [provided by RefSeq, Sep 2012]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 1-17395867-G-A is Benign according to our data. Variant chr1-17395867-G-A is described in ClinVar as [Benign]. Clinvar id is 704516.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PADI6	NM_207421.4	c.1618+204G>A		intron_variant		ENST00000619609.1	NP_997304.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PADI6	ENST00000619609.1	c.1618+204G>A		intron_variant		1	NM_207421.4	ENSP00000483125	P1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55279 AN: 151932 Hom.: 10197 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.364 AC: 55315 AN: 152052 Hom.: 10202 Cov.: 33 AF XY: 0.369 AC XY: 27393 AN XY: 74330

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.339

Alfa AF: 0.361 Hom.: 18738

Bravo AF: 0.355

Asia WGS AF: 0.284 AC: 988 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 02, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.35

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: rs7538876; hg19: chr1-17722363;