rs6916092

Variant names:

• chr6-63559942-G-A
• rs6916092
• NM_001385254.1:c.-445-16494G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-63559942-G-A
• chr6-63559942-G-T

Variant summary

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

The NM_001385254.1(PTP4A1):​c.-445-16494G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,838 control chromosomes in the GnomAD database, including 5,748 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 0.25 (5748 hom., cov: 31)
• Consequence: PTP4A1 NM_001385254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 2 publications found

Genes affected

PTP4A1 (HGNC:9634): (protein tyrosine phosphatase 4A1) This gene encodes a member of a small class of prenylated protein tyrosine phosphatases (PTPs), which contain a PTP domain and a characteristic C-terminal prenylation motif. The encoded protein is a cell signaling molecule that plays regulatory roles in a variety of cellular processes, including cell proliferation and migration. The protein may also be involved in cancer development and metastasis. This tyrosine phosphatase is a nuclear protein, but may associate with plasma membrane by means of its prenylation motif. Pseudogenes related to this gene are located on chromosomes 1, 2, 5, 7, 11 and X. [provided by RefSeq, Jun 2013]

LGSN (HGNC:21016): (lengsin, lens protein with glutamine synthetase domain) This gene encodes a protein with similarity to the GS I members of the glutamine synthetase superfamily. The encoded protein is referred to as a pseudo-glutamine synthetase because it has no glutamine synthesis activity and may function as a chaperone protein. This protein is localized to the lens and may be associated with cataract disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]

ENSG00000289911 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385254.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTP4A1	NM_001385254.1		c.-445-16494G>A		intron	N/A	NP_001372183.1	Q93096
	PTP4A1	NM_001385255.1		c.-446+9449G>A		intron	N/A	NP_001372184.1	Q93096
	PTP4A1	NM_001385256.1		c.-445-16494G>A		intron	N/A	NP_001372185.1	Q93096

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTP4A1	ENST00000648894.1		c.-445-16494G>A		intron	N/A	ENSP00000497588.1	Q93096
	PTP4A1	ENST00000639568.2	TSL:5	c.-446+9449G>A		intron	N/A	ENSP00000497431.1	A0A3B3ISR8
	PTP4A1	ENST00000470661.1	TSL:2	n.333-16494G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38446 AN: 151720 Hom.: 5741 Cov.: 31

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.253 AC: 38452 AN: 151838 Hom.: 5748 Cov.: 31 AF XY: 0.253 AC XY: 18768 AN XY: 74184

African (AFR) AF: 0.0850 AC: 3519 AN: 41424

American (AMR) AF: 0.337 AC: 5131 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1280 AN: 5142

South Asian (SAS) AF: 0.305 AC: 1467 AN: 4804

European-Finnish (FIN) AF: 0.247 AC: 2597 AN: 10506

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22458 AN: 67934

Other (OTH) AF: 0.273 AC: 577 AN: 2112

Alfa AF: 0.290 Hom.: 4430

Bravo AF: 0.253

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6916092; hg19: chr6-64269847;