chr9-94096129-G-A

Position:

• chr9-94096129-G-A

Variant summary

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

The NM_001253829.2(PTPDC1):​c.754+675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,674 control chromosomes in the GnomAD database, including 25,965 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 0.57 (25965 hom., cov: 33)
• Consequence: PTPDC1 NM_001253829.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

PTPDC1 (HGNC:30184): (protein tyrosine phosphatase domain containing 1) The protein encoded by this gene contains a characteristic motif of protein tyrosine phosphatases (PTPs). PTPs regulate activities of phosphoproteins through dephosphorylation. They are signaling molecules involved in the regulation of a wide variety of biological processes. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTPDC1	NM_001253829.2	c.754+675G>A		intron_variant		ENST00000620992.5	NP_001240758.1
PTPDC1	NM_001253830.2	c.592+675G>A		intron_variant			NP_001240759.1
PTPDC1	NM_152422.4	c.748+675G>A		intron_variant			NP_689635.3
PTPDC1	NM_177995.3	c.592+675G>A		intron_variant			NP_818931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTPDC1	ENST00000620992.5	c.754+675G>A		intron_variant		2	NM_001253829.2	ENSP00000477817
PTPDC1	ENST00000288976.3	c.748+675G>A		intron_variant		1		ENSP00000288976
PTPDC1	ENST00000375360.7	c.592+675G>A		intron_variant		1		ENSP00000364509	P1
PTPDC1	ENST00000650567.1	c.592+675G>A		intron_variant				ENSP00000497158	P1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86820 AN: 151556 Hom.: 25924 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.573 AC: 86917 AN: 151674 Hom.: 25965 Cov.: 33 AF XY: 0.572 AC XY: 42435 AN XY: 74130

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.582

Alfa AF: 0.498 Hom.: 31456

Bravo AF: 0.595

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.71

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: rs6479527; hg19: chr9-96858411;